The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
NATIONAL LIBRARY OF MEDICINE service for health professionals and consumers. It links extensive information from the National Institutes of Health and other reviewed sources of information on specific diseases and conditions.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Exclusive legal rights or privileges applied to inventions, plants, etc.
A novel composition, device, or process, independently conceived de novo or derived from a pre-existing model.
Property, such as patents, trademarks, and copyright, that results from creative effort. The Patent and Copyright Clause (Art. 1, Sec. 8, cl. 8) of the United States Constitution provides for promoting the progress of science and useful arts by securing for limited times to authors and inventors, the exclusive right to their respective writings and discoveries. (From Black's Law Dictionary, 5th ed, p1014)
A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The systematic study of the complete DNA sequences (GENOME) of organisms.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Tumors or cancer of the PROSTATE.
Mutant mice homozygous for the recessive gene "nude" which fail to develop a thymus. They are useful in tumor studies and studies on immune responses.
A gland in males that surrounds the neck of the URINARY BLADDER and the URETHRA. It secretes a substance that liquefies coagulated semen. It is situated in the pelvic cavity behind the lower part of the PUBIC SYMPHYSIS, above the deep layer of the triangular ligament, and rests upon the RECTUM.
In vivo methods of screening investigative anticancer drugs, biologic response modifiers or radiotherapies. Human tumor tissue or cells are transplanted into mice or rats followed by tumor treatment regimens. A variety of outcomes are monitored to assess antitumor effectiveness.
A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
Genes at loci that are involved in the development of WILMS TUMOR. Included are human WT1 at 11p13 and human WT2 (MTACR1) at 11p15.
The local recurrence of a neoplasm following treatment. It arises from microscopic cells of the original neoplasm that have escaped therapeutic intervention and later become clinically visible at the original site.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
Branch of medicine concerned with the prevention and control of disease and disability, and the promotion of physical and mental health of the population on the international, national, state, or municipal level.
Tumors or cancer of the human BREAST.
An agent with anti-androgen and progestational properties. It shows competitive binding with dihydrotestosterone at androgen receptor sites.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)
Tumors or cancer of the SKIN.
The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.
The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements.
A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
Health insurance coverage for all persons in a state or country, rather than for some subset of the population. It may extend to the unemployed as well as to the employed; to aliens as well as to citizens; for pre-existing conditions as well as for current illnesses; for mental as well as for physical conditions.
The application of medical knowledge to questions of law.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Scientific study of human skeletal remains with the express purpose of identification. This includes establishing individual identity, trauma analysis, facial reconstruction, photographic superimposition, determination of time interval since death, and crime-scene recovery. Forensic anthropologists do not certify cause of death but provide data to assist in determination of probable cause. This is a branch of the field of physical anthropology and qualified individuals are certified by the American Board of Forensic Anthropology. (From Am J Forensic Med Pathol 1992 Jun;13(2):146)
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
The application of genetic analyses and MOLECULAR DIAGNOSTIC TECHNIQUES to legal matters and crime analysis.
Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.
The study of microorganisms such as fungi, bacteria, algae, archaea, and viruses.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. (1/41147)

DNA or oligonucleotide arrays are widely used for large-scale expression measurements, using various implementations: macroarrays in which DNA is spotted onto nylon membranes of relatively large dimensions (with radioactive detection) on the one hand; microarrays on glass slides and oligonucleotide chips, both used with fluorescent probes, on the other hand. Nylon micro-arrays with colourimetric detection have also been described recently. The small physical dimensions of miniaturized systems allow small hybridization volumes (2-100 microl) and provide high probe concentrations, in contrast to macroarrays. We show, however, that actual sensitivity (defined as the amount of sample necessary for detection of a given mRNA species) is in fact similar for all these systems and that this is mostly due to the very different amounts of target material present on the respective arrays. We then demonstrate that the combination of nylon microarrays with(33)P-labelled radioactive probes provides 100-fold better sensitivity, making it possible to perform expression profiling experiments using submicrogram amounts of unamplified total RNA from small biological samples. This has important implications in basic and clinical research and makes this alternative approach particularly suitable for groups operating in an academic context.  (+info)

On-line monitoring of gene expression. (2/41147)

Gene expression in cultures of Escherichia coli has been determined in situ and on-line by the use of an electrochemical sensor. Intact bacteria were used to monitor the induction of the lacZ gene; the onset of stationary phase was also monitored, using a reporter gene fused to the RpoS-dependent promoter of the osmY gene. The technique described can in principle be used to determine the activity of any promoter, with a variety of reporter genes. This technology is non-intrusive, allows real-time monitoring of gene expression, and will be useful in the study of growth regulation and development.  (+info)

Computational methods for the identification of differential and coordinated gene expression. (3/41147)

With the first complete 'draft' of the human genome sequence expected for Spring 2000, the three basic challenges for today's bioinformatics are more than ever: (i) finding the genes; (ii) locating their coding regions; and (iii) predicting their functions. However, our capacity for interpreting vertebrate genomic and transcript (cDNA) sequences using experimental or computational means very much lags behind our raw sequencing power. If the performances of current programs in identifying internal coding exons are good, the precise 5'-->3' delineation of transcription units (and promoters) still requires additional experiments. Similarly, functional predictions made with reference to previously characterized homologues are leaving >50% of human genes unannotated or classified in uninformative categories ('kinase', 'ATP-binding', etc.). In the context of functional genomics, large-scale gene expression studies using massive cDNA tag sequencing, two-dimensional gel proteome analysis or microarray technologies are the only approaches providing genome-scale experimental information at a pace consistent with the progress of sequencing. Given the difficulty and cost of characterizing genes one by one, academic and industrial researchers are increasingly relying on those methods to prioritize their studies and choose their targets. The study of expression patterns can also provide some insight into the function, reveal regulatory pathways, indicate side effects of drugs or serve as a diagnostic tool. In this article, I review the theoretical and computational approaches used to: (i) identify genes differentially expressed (across cell types, developmental stages, pathological conditions, etc.); (ii) identify genes expressed in a coordinated manner across a set of conditions; and (iii) delineate clusters of genes sharing coherent expression features, eventually defining global biological pathways.  (+info)

Genome-wide expression profiling in Escherichia coli K-12. (4/41147)

We have established high resolution methods for global monitoring of gene expression in Escherichia coli. Hybridization of radiolabeled cDNA to spot blots on nylon membranes was compared to hybridization of fluorescently-labeled cDNA to glass microarrays for efficiency and reproducibility. A complete set of PCR primers was created for all 4290 annotated open reading frames (ORFs) from the complete genome sequence of E.coli K-12 (MG1655). Glass- and nylon-based arrays of PCR products were prepared and used to assess global changes in gene expression. Full-length coding sequences for array printing were generated by two-step PCR amplification. In this study we measured changes in RNA levels after exposure to heat shock and following treatment with isopropyl-beta-D-thiogalactopyranoside (IPTG). Both radioactive and fluorescence-based methods showed comparable results. Treatment with IPTG resulted in high level induction of the lacZYA and melAB operons. Following heat shock treatment 119 genes were shown to have significantly altered expression levels, including 35 previously uncharacterized ORFs and most genes of the heat shock stimulon. Analysis of spot intensities from hybridization to replicate arrays identified sets of genes with signals consistently above background suggesting that at least 25% of genes were expressed at detectable levels during growth in rich media.  (+info)

Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. (5/41147)

mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF(+) strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.  (+info)

NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae. (6/41147)

Analysis of global gene expression in Saccharomyces cerevisiae by the serial analysis of gene expression technique has permitted the identification of at least 302 previously unidentified transcripts from nonannotated open reading frames (NORFs). Transcription of one of these, NORF5/HUG1 (hydroxyurea and UV and gamma radiation induced), is induced by DNA damage, and this induction requires MEC1, a homolog of the ataxia telangiectasia mutated (ATM) gene. DNA damage-specific induction of HUG1, which is independent of the cell cycle stage, is due to the alleviation of repression by the Crt1p-Ssn6p-Tup1p complex. Overexpression of HUG1 is lethal in combination with a mec1 mutation in the presence of DNA damage or replication arrest, whereas a deletion of HUG1 rescues the lethality due to a mec1 null allele. HUG1 is the first example of a NORF with important biological functional properties and defines a novel component of the MEC1 checkpoint pathway.  (+info)

Microarray analysis of replicative senescence. (7/41147)

BACKGROUND: Limited replicative capacity is a defining characteristic of most normal human cells and culminates in senescence, an arrested state in which cells remain viable but display an altered pattern of gene and protein expression. To survey widely the alterations in gene expression, we have developed a DNA microarray analysis system that contains genes previously reported to be involved in aging, as well as those involved in many of the major biochemical signaling pathways. RESULTS: Senescence-associated gene expression was assessed in three cell types: dermal fibroblasts, retinal pigment epithelial cells, and vascular endothelial cells. Fibroblasts demonstrated a strong inflammatory-type response, but shared limited overlap in senescent gene expression patterns with the other two cell types. The characteristics of the senescence response were highly cell-type specific. A comparison of early- and late-passage cells stimulated with serum showed specific deficits in the early and mid G1 response of senescent cells. Several genes that are constitutively overexpressed in senescent fibroblasts are regulated during the cell cycle in early-passage cells, suggesting that senescent cells are locked in an activated state that mimics the early remodeling phase of wound repair. CONCLUSIONS: Replicative senescence triggers mRNA expression patterns that vary widely and cell lineage strongly influences these patterns. In fibroblasts, the senescent state mimics inflammatory wound repair processes and, as such, senescent cells may contribute to chronic wound pathologies.  (+info)

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. (8/41147)

DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290 E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated under this growth condition, consistent with known patterns of growth rate-dependent regulation and increased rate of protein synthesis in rapidly growing cells. The cells grown on minimal medium showed significantly elevated expression of many genes involved in biosynthesis of building blocks, most notably the amino acid biosynthetic pathways. Nearly half of the known RpoS-dependent genes were expressed at significantly higher levels in minimal medium than in rich medium, and rpoS expression was similarly elevated. The role of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark features of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protection of the cells from acid stress. A hypothesis invoking RpoS and UspA (universal stress protein, also significantly elevated in minimal glucose medium) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.  (+info)

Abstract Background Conventional differential gene expression analysis by methods such as students t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i.e., protein-protein interactions) for biological network inference. We propose a novel differentially weighted graphical LASSO (dwgLASSO) algorithm that builds group-specific networks and perform network-based differential gene expression analysis to select biomarker candidates by considering their topological differences between the groups. Results Through simulation, we showed that wgLASSO can achieve better performance in building biologically relevant networks than ...
Gene Expression Profiling Analysis of Bisphenol A-Induced Perturbation in Biological Processes in ER-Negative HEK293 Cells. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The heterogeneity of prostate cancers extends within clinical states and across states. At the extreme ends of the clinical spectrum are prognostically favorable localized tumors with a low biological potential for metastasis and tumors with a high propensity for early dissemination that are invariably lethal. These clinical phenotypes are related in part to the intrinsic biology of tumor cells and are reflected in the pattern of expression of specific genes. Using comprehensive gene expression analysis of tumor samples representing the nonmetastatic and metastatic phenotypes, we identified genes that were consistently and strongly differentially expressed and represent common and valid biological differences underlying clinical heterogeneity.. Few prior studies have used high-throughput gene expression analysis to study prostate cancer metastases. One reason is that well-preserved surgical tissue samples of metastatic prostate cancer are rare, which limits the availability of appropriate ...
Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n = 101) and/or poor quality control criteria (n = 10) (test set). With 10-marker classifiers, all training set samples as well as 97 of the 101 test
Osteoarthritis (OA) is characterized by alterations to subchondral bone as well as articular cartilage. Changes to bone in OA have also been identified at sites distal to the affected joint, which include increased bone volume fraction and reduced bone mineralization. Altered bone remodelling has been proposed to underlie these bone changes in OA. To investigate the molecular basis for these changes, we performed microarray gene expression profiling of bone obtained at autopsy from individuals with no evidence of joint disease (control) and from individuals undergoing joint replacement surgery for either degenerative hip OA, or fractured neck of femur (osteoporosis [OP]). The OP sample set was included because an inverse association, with respect to bone density, has been observed between OA and the low bone density disease OP. Compugen human 19K-oligo microarray slides were used to compare the gene expression profiles of OA, control and OP bone samples. Four sets of samples were analyzed, comprising 10
Since their first use nearly fifteen years ago [1], microarray gene expression profiling experiments have become a ubiquitous tool in the study of disease. The vast number of gene transcripts assayed by modern microarrays (105-106) has driven forward our understanding of biological processes tremendously, elucidating the genes and regulatory mechanisms that drive specific phenotypes. However, the high-dimensional data produced in these experiments--often comprising many more variables than samples and subject to noise--also presents analytical challenges.. The analysis of gene expression data can be broadly grouped into two categories: the identification of differentially expressed genes (or gene-sets) between two or more known conditions, and the unsupervised identification (clustering) of samples or genes that exhibit similar profiles across the data set. In the former case, each gene is tested individually for association with the phenotype of interest, adjusting at the end for the vast ...
A peripheral blood gene expression score is associated with plaque volume and phenotype by intravascular ultrasound with radiofrequency backscatter analysis: results from the ATLANTA study
TY - JOUR. T1 - Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma. T2 - A report from the International DLBCL Rituximab-CHOP Consortium Program Study. AU - Visco, C.. AU - Li, Y.. AU - Xu-Monette, Z. Y.. AU - Miranda, R. N.. AU - Green, T. M.. AU - Li, Y.. AU - Tzankov, A.. AU - Wen, W.. AU - Liu, W. M.. AU - Kahl, B. S.. AU - DAmore, E. S.G.. AU - Montes-Moreno, S.. AU - Dybkær, K.. AU - Chiu, A.. AU - Tam, W.. AU - Orazi, A.. AU - Zu, Y.. AU - Bhagat, G.. AU - Winter, J. N.. AU - Wang, H. Y.. AU - ONeill, S.. AU - Dunphy, C. H.. AU - Hsi, E. D.. AU - Zhao, X. F.. AU - Go, R. S.. AU - Choi, W. W.L.. AU - Zhou, F.. AU - Czader, M.. AU - Tong, J.. AU - Zhao, X.. AU - Van Krieken, J. H.. AU - Huang, Q.. AU - Ai, W.. AU - Etzell, J.. AU - Ponzoni, M.. AU - Ferreri, A. J.M.. AU - Piris, M. A.. AU - Møller, M. B.. AU - Bueso-Ramos, C. E.. AU - Medeiros, L. ...
Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma: a report from the International DLBCL Rituximab-CHOP Consortium Program Study.
Abstract: Association rules mining methods have been recently applied to gene expression data analysis to reveal relationships between genes and different conditions and features. However, not much effort has focused on detecting the relation between gene expression maps and related gene functions. Here we describe such an approach to mine association rules among gene functions in clusters of similar gene expression maps on mouse brain. The experimental results show that the detected association rules make sense biologically. By inspecting the obtained clusters and the genes having the gene functions of frequent itemsets, interesting clues were discovered that provide valuable insight to biological scientists. Moreover, discovered association rules can be potentially used to predict gene functions based on similarity of gene expression maps.. ...
Purpose: Retinopathy of prematurity (ROP) is a common blinding disease caused by the abnormal growth of blood vessels in the retina of premature babies with low birth weight and low gestation period. However, the mechanisms and factors contributing to the progression of ROP are still unknown. The present study aimed to identify gene(s) responsible for ROP progression by a global gene expression profiling.. Methods: From a cohort of 600 subjects comprising ROP babies (n=350) and controls (n=250), 15 ROP babies at any stage (gestational age [GA] ≤ 35 weeks and/or birth weight [BW] ≤ 1700 g) and premature babies with no ROP (n=6) (GA ≤ 35 weeks and/or BW ≤ 1700 g) and full term babies of the same age and no ROP (n=3), were screened. RNA was isolated from 0.5-1 ml of blood using RNeasy mini kit from Qiagen and the purity and integrity of RNA was checked with Bioanalyzer 2100 (Agilent). Global gene expression profiling was performed by using Illumina bead Chip array having ~47,000 ...
TY - JOUR. T1 - Self-organizing latent lattice models for temporal gene expression profiling. AU - Zhang, Byoung Tak. AU - Yang, Jinsan. AU - Chi, Sung Wook. N1 - Funding Information: This work was supported by the Korean Government through BK21-IT, BrainTech, IMT2000 Bioinformatics and NRL Programs.. PY - 2003/7. Y1 - 2003/7. N2 - DNA microarrays are a high-throughput technology useful for functional genomics and gene expression analysis. While many microarray data are generated in sequence, most expression analysis tools are not utilizing the temporal information. Temporal expression profiling is important in many applications, including developmental studies, pathway analysis, and disease prognosis. In this paper, we develop a learning method designed for temporal gene expression profiling from massive DNA-microarray data. It attempts to learn probabilistic lattice maps of the gene expressions, which are then used for profiling the trajectories of temporal expressions of co-regulated genes. ...
Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks
Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish.
The increased use of microarray expression profiling to study both the molecular biology of cancer and the cellular physiology of difficult-to-isolate cell types has led to a growing need for methods that allow the use of limiting quantities of RNA. This limitation has prompted the development of amplification methods that produce the quantities of RNA required for microarray analysis. Efforts have become increasingly focused upon developing a protocol that minimizes amplification bias, provides versatility, and reduces technical complexity. We evaluated the new protocol Transplex™ Whole Transcriptome Amplification (WTA) produced by Rubicon Genomics. The kit was tested on Human Reference RNA (Stratagene) and on RNA extracted from a renal tumor cell line. Reproducibility, sensitivity and reliability in calling differentially expressed genes were evaluated by both Real-Time PCR and GeneChip® technology (Affymetrix). We tested reproducibility by comparing the expression profiles provided by U133 ...
Association rules mining methods have been recently applied to gene expression data analysis to reveal relationships between genes and different conditions and features. However, not much effort has focused on detecting the relation between gene expression maps and related gene functions. Here we describe such an approach to mine association rules among gene functions in clusters of similar gene expression maps on mouse brain. The experimental results show that the detected association rules make sense biologically.
Seker, H. (2004) A Multi-Fuzzy Filtering Approach to Reliable Gene Expression Profile Analysis. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, October 2004, pp. 37-40 ...
APC (Adenomatous polyposis coli) plays an important role in the pathogenesis of both familial and sporadic colorectal cancer. Patients carrying germline APC mutations develop multiple colonic adenomas at younger age and higher frequency than non-carrier cases which indicates that silencing of one APC allele may be sufficient to initiate the transformation process. To elucidate the biological dysregulation underlying adenoma formation we examined global gene expression profiles of adenomas and corresponding normal mucosa from an FAP patient. Differential expression of the most significant gene identified in this study was further validated by mRNA in situ hybridization, reverse transcriptase PCR and Northern blotting in different sets of adenomas, tumours and cancer cell lines. Eighty four genes were differentially expressed between all adenomas and corresponding normal mucosa, while only seven genes showed differential expression within the adenomas. The first group included pregnancy specific β-1
Background: Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Methods: Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Results: Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the ...
Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA. In the field of virology, when analyzing the host cells reaction to infection, the often high representation of viral RNA (vRNA) within total RNA preparations from infected cells is likely to interfere with microarray analysis. Yet, this effect has not been investigated despite the many reports that describe gene expression profiling of virus-infected cells using microarrays. In this study we used coronaviruses as a model to show that vRNA indeed interferes with microarray analysis, decreasing both sensitivity and accuracy. We also demonstrate that the removal of vRNA from total RNA samples, by means of virus-specific oligonucleotide capturing, significantly reduced the number of false-positive hits and increased the sensitivity of the method as tested on different array platforms. We therefore
Purpose This article provides a review of the transcriptomic expression profiling studies that have been performed on meningiomas so far. We discuss some future prospects and challenges ahead in the field of gene expression profiling. Methods We performed a systematic search in the PubMed and EMBASE databases in May 2010 using the following search terms alone or in combination: meningioma, microarray analysis, oligonucleotide array sequence analysis, or gene expression profiling. Only original research articles in English that had used RNA hybridized to high-resolution microarray chips to generate gene expression profiles were included. Results We identified 13 articles matching the inclusion criteria. All studies had been performed during the last decade. Conclusions The main results of the studies can be grouped in three categories: (1) several groups have identified meningioma-specific genes and genes associated with the three WHO grades, and the main histological subtypes of grade I ...
Observation of gene expression changes implying gene regulations using a repetitive experiment in time course has become more and more important. However, there is no effective method which can handle such kind of data. For instance, in a clinical/biological progression like inflammatory response or cancer formation, a great number of differentially expressed genes at different time points could be identified through a large-scale microarray approach. For each repetitive experiment with different samples, converting the microarray datasets into transactional databases with significant singleton genes at each time point would allow sequential patterns implying gene regulations to be identified. Although traditional sequential pattern mining methods have been successfully proposed and widely used in different interesting topics, like mining customer purchasing sequences from a transactional database, to our knowledge, the methods are not suitable for such biological dataset because every transaction in
Background Parkinsons disease (PD) is affecting 5 million people worldwide, but the response mechanisms of the striatum are still unclear. Therefore, identification of gene expression alterations in...
Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the transition phase 170 genes were differentially expressed, and 717 genes were differentially expressed between the transition and the
BACKGROUND: Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro ...
The identification of a prognostic gene expression signature in breast cancer that is valid across multiple independent data sets and different microarray platforms is a challenging problem [1]. Recently, there have been reports of molecular prognostic and predictive signatures that were also valid in external independent cohorts [2-7]. One of these studies derived the prognostic signature from genes correlating with histological grade [4], while in [5] it was derived directly from correlations with clinical outcome data and was validated in estrogen receptor positive lymph node negative (ER+LN-) breast cancer. Another study validated a predictive score, based on 21 genes, for ER+LN-tamoxifen treated breast cancer [2]. These results are encouraging, yet, as explained recently in [8, 9], much larger cohort sizes may be needed before a consensus prognostic signature emerges. While the intrinsic subtype classification does appear to constitute a set of consensus signatures [7], it is also clear ...
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EpiRegNet aims to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields ...
1. Chockalingm A, Campbell NR, Fodor JG. Worldwide epidemic of hypertension. Can J Cardio. 2006;22:553-555 2. Tomson J, Lip GYH. Blood Pressure demographic: nature or nurture…… genes or environment?. BMC Med. 2005;3:3 3. WHO. World Health Report 2002: Reducing Risks, Promoting Healthy life. Geneva: World Health Organization. 2002 4. Heller RA. et al. Discovery and analysis of inflammatory disease related genes using cDNA microarrays. Proc Nat Acad Sci. 1997;94:2150- 2155 5. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996;14:1675-80 6. Tzouvelekis A, Patlakas G, Bouros D. Application of Microarray Technology in pulmonary diseases. Respir Res. 2004;5:26 7. King HC, Sinha AA. Gene expression profile analysis by DNA microarrays: promise and pitfalls. JAMA. 2001;286:2280-2288 8. LI JJ. Inflammation in hypertension: primary ...
Microarray gene expression data sets are jointly analyzed to increase statistical power. They could either be merged together or analyzed by meta-analysis. For a given ensemble of data sets, it cannot be foreseen which of these paradigms, merging or meta-analysis, works better. In this article, three joint analysis methods, Z-score normalization, ComBat and the inverse normal method (meta-analysis) were selected for survival prognosis and risk assessment of breast cancer patients. The methods were applied to eight microarray gene expression data sets, totaling 1324 patients with two clinical endpoints, overall survival and relapse-free survival. The performance derived from the joint analysis methods was evaluated using Cox regression for survival analysis and independent validation used as bias estimation. Overall, Z-score normalization had a better performance than ComBat and meta-analysis. Higher Area Under the Receiver Operating Characteristic curve and hazard ratio were also obtained when ...
This project is an investigation of whether analysing subsets of time series gene expression data can give additional information about putatively co-regulated genes, compared to only using the whole time series. The original gene expression data set was partitioned into subsets and similarity was computed for both the whole timed series and subsets. Pearson correlation was used as similarity measure between gene expression profiles. The results indicate that analysing co-expression in subsets of gene expression data derives true-positive connections, with respect to co-regulation, that are not detected by only using the whole time series data. Unfortunately, with the actual data set, chosen similarity measure and partitioning of the data, randomly generated connections have the same amount of true-positives as the ones derived by the applied analysis. However, it is worth to continue further analysis of the subsets of gene expression data, which is based on the multi-factorial nature of gene ...
Preface. Acknowledgments.. 1 Introduction.. 1.1 Basic Terminology.. 1.1.1 The Central Dogma of Molecular Biology.. 1.1.2 Genome.. 1.1.3 Proteome.. 1.1.4 DNA (Deoxyribonucleic Acid).. 1.1.5 RNA (Ribonucleic Acid).. 1.1.6 mRNA (messenger RNA).. 1.1.7 Genetic Code.. 1.1.8 Gene.. 1.1.9 Gene Expression and the Gene Expression Level.. 1.1.10 Protein.. 1.2 Overlapping Areas of Research.. 1.2.1 Genomics.. 1.2.2 Proteomics.. 1.2.3 Bioinformatics.. 1.2.4 Transcriptomics and Other -omics.. 1.2.5 Data Mining.. 2 Basic Analysis of Gene Expression Microarray Data.. 2.1 Introduction.. 2.2 Microarray Technology.. 2.2.1 Spotted Microarrays.. 2.2.2 Affymetrix GeneChip® Microarrays.. 2.2.3 Bead-Based Microarrays.. 2.3 Low-Level Preprocessing of Assymetrix Microarrays.. 2.3.1 MAS5.. 2.3.2 RMA.. 2.3.3 GCRMA.. 2.3.4 PLIER.. 2.4 Public Repositories of Microarray Data.. 2.4.1 Microarray Gene Expression Data Society (MGED) Standards.. 2.4.2 Public Databases.. 2.4.2.1 Gene Expression Omnibus (GEO).. 2.4.2.2 ...
Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
CG000170_TechNote_BiologicalandTechnicalVariationinSingleCell3GeneExpressionExperiments_RevA_.pdf. Technical Note - Biological & Technical Variation in Single Cell Gene Expression Experiments. The Chromium Single Cell 3′ v2 Reagent Kits protocol (Document CG00052) produces Single Cell 3′ short-read sequencer compatible libraries. Technical and biological variation may be present in the experiment design, and may impact data interpretation. Potential sources of technical variation include running a sample on two separate microfluidic chips or at different well positions on the same chip, and or technical variation introduced by sequencing libraries on separate Illumina flowcells or sequencing lanes. This Technical Note examines the potential sources of technical and biological variation and their effects on single cell gene expression. These factors need to be considered when designing an experiment to minimize bias and generate reliable single cell gene expression data.. FOR USE WITH. ...
Background & objective: Microarray and next generation sequencing (NGS) data are the important sources to find helpful molecular patterns. Also, the great number of gene expression data increases the challenge of how to identify the biomarkers associated with cancer. The random forest (RF) is used to effectively analyze the problems of large-p and small-n. Therefore, RF can be used to select and rank the genes for the diagnosis and effective treatment of cancer. Methods: The microarray gene expression data of colon, leukemia, and prostate cancers were collected from public databases. Primary preprocessing was done on them using limma package, and then, the RF classification method was implemented on datasets separately in R software. Finally, the selected genes in each of the cancers were evaluated and compared with those of previous experimental studies and their functionalities were assessed in molecular cancer processes. Result: The RF method extracted very small sets of genes while it retained its
Breast cancer is the most common malignancy among women in the United States with the second highest incidence of cancer-related death following lung cancer. The decision-making process regarding adjuvant therapy is a time intensive dialogue between the patient and her oncologist. There are multiple tools that help individualize the treatment options for a patient. Population-based analysis with Adjuvant! Online and genomic profiling with Oncotype DX are two commonly used tools in patients with early stage, node-negative breast cancer. This case report illustrates a situation in which the population-based prognostic and predictive information differed dramatically from that obtained from genomic profiling and affected the patients decision. In light of this case, we discuss the benefits and limitations of these tools.
For more than a decade, global gene expression profiling has been extensively used to elucidate the biology of human papillomaviruses (HPV) and their role in cervical- and head-and-neck cancers. Since 2008, the expression profiling of miRNAs has been reported in multiple HPV studies. Two major strategies have been employed in the gene and miRNA profiling studies: In the first approach, HPV positive tumors were compared to normal tissues or to HPV negative tumors. The second strategy relied on analysis of cell cultures transfected with single HPV oncogenes or with HPV genomes compared to untransfected cells considered as models for the development of premalignant and malignant transformations.. In this review, we summarize what we have learned from a decade of global expression profiling studies. We performed comprehensive analysis of the overlap of the lists of differentially expressed genes and microRNAs, in both tissue samples and cell culture based studies. The review focuses mainly on HPV16, ...
A meta-analysis was performed across six public microarray datasets for human small cell lung cancer (SCLC) comprising 365 samples across eight different platforms. Genes were ranked according to effect size and p-value for tumor versus control samples, and false discovery rates were calculated. The top scoring 48 genes that were significant by both methods, along with the 48 highest rated surface antigen genes, were used to populate a gene list for subsequent single cell evaluation. High throughput gene expression analysis was performed for 400 individual cells from one SCLC line (H446) using the Fluidigm microfluidic platform. Supervised machine learning was applied to identify transcriptionally-defined subgroups among these cells. The non-parametric Kolmogorov-Smirnov test was then used to determine those surface markers best able to distinguish each cluster. Individual cells from each group were then FACS-isolated, and clonogenicity was evaluated after 14 days in culture. Using these surface ...
Title: Definition of Genes and Paths Involved in Alzheimers Disease: Using Gene Expression Profiles and Chemical Genetics at the Mouse Brain Level. VOLUME: 7 ISSUE: 5. Author(s):Pu Wu and Yinghe Hu. Affiliation:Key Lab of Brain Functional GenomicsMOE STCSM; Shanghai Institute of Brain Functional Ge-nomics, East China Normal University, 3663 Zhongshan Road N. Shanghai, 200062, China.. Keywords:cDKO mice, SNAP-25, hypothalamus, neuronal plasticity, NMDA receptor. Abstract: Gene expression profiling of a number of distinct brain regions under different behavioral and biological states was analyzed using DNA microarray technology. These included hippocampal development, aging process, environ-mental enrichment, fear conditioning, and calorie restriction. Our results identified numerous genes and signal pathways that may play critical roles in learning and memory, brain aging and longevity. Furthermore, chemical genetic approach combined with gene expression profiling analysis was applied to study ...
Gene expression profiling classifies individual tumors by their gene expression patterns and may also describe and predict therapeutic resistance and sensitivity patterns. Profiling in several cancers, such as breast cancer, colon cancer, lymphoma, leukemia, and melanoma [3], has already identified molecular subclasses of tumors. Identification of tumor subtypes may be predictive for prognosis or response to drug therapy [6, 7, 28-31].. The potential of routine gene expression profiling to predict clinical outcomes for cancer patients has yet to be determined. The Evaluation of Genomic Applications in Practice and Prevention Working Group stated in 2009 that there was insufficient evidence to make a recommendation for or against the use of tumor gene expression profiles to improve outcomes in defined populations of women with breast cancer [32]. Clearly, more work needs to be done to translate promising research findings into clinically relevant results.. Comparison of FFPET sample-derived ...
Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count
Cancer is a disease characterized by uncontrolled cell growth and proliferation. For cancer to develop, genes regulating cell growth and differentiation must be altered; these mutations are then maintained through subsequent cell divisions and are thus present in all cancerous cells. Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. In the context of cancer, gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression profiling often helps in predicting the patients clinical outcome. Oncogenesis is the process by which normal cells acquire the properties of cancer cells leading to the formation of a cancer or tumor (see: tumorigenesis). It is characterized by a molecular reprogramming of a cell to undergo uninhibited cell division, allowing the formation of a malignant mass. The cells forming this mass undergo natural selection: as cells acquire mutations ...
Botling J, Edlund K, Lohr M, Hellwig B, Holmberg L, Lambe M, Berglund A, Ekman S, Bergqvist M, Pontén F, König A, Fernandes O, Karlsson M, Helenius G, Karlsson C, Rahnenführer J, Hengstler JG, Micke P Clin. Cancer Res. 19 (1) 194-204 [2013-01-01; online 2012-10-04] Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap. Here, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P , ...
Large amounts of information generated by gene expression profiling will increase implementation of data management tools Gene expression profiling can...
Welcome to the homepage of the GenT er mining tool! GenT er is an application tool for alignment, analysis and mining of gene expression time series. The core algorithm is based on dynamic time warping techniques used in the speech recognition field(1). These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases, as demonstrated on the figure below.. ...
DI-fusion, le Dépôt institutionnel numérique de lULB, est loutil de référencementde la production scientifique de lULB.Linterface de recherche DI-fusion permet de consulter les publications des chercheurs de lULB et les thèses qui y ont été défendues.
Discovering robust prognostic gene signatures as biomarkers using genomics data can be challenging. We have developed a simple but efficient method for discovering prognostic biomarkers in cancer gene expression data sets using modules derived from a highly reliable gene functional interaction network. When applied to breast cancer, we discover a novel 31-gene signature associated with patient survival. The signature replicates across 5 independent gene expression studies, and outperforms 48 published gene signatures. When applied to ovarian cancer, the algorithm identifies a 75-gene signature associated with patient survival. A Cytoscape plugin implementation of the signature discovery method is available at http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin
In the present study, we established a novel TNBC classification system, the FUSCC classification, by integrating the expression profiles of both mRNAs and lncRNAs. TNBC samples can be clearly classified into four subtypes according to our system: IM, LAR, MES, and BLIS. Each subtype has its own unique transcriptome profile. Furthermore, we filtrated out several subtype-specific lncRNAs and predicted possible functions of these lncRNAs in TNBC biological processes by analyzing the co-expression network between lncRNAs and mRNAs. To the best of our knowledge, the present study is the first to develop a novel TNBC classification system based on the transcriptome profiles of both mRNAs and lncRNAs in a large TNBC cohort.. Several novel findings were revealed in our in-depth transcriptome analysis. First, considering the expanding roles of lncRNAs in tumorigenesis and disease development, we integrated the expression profiles of both mRNAs and lncRNAs in an attempt to comprehensively understand the ...
Gene co-expression network analysis of transcriptome data has enabled the identification of key genes and important networks underlying complex production and disease traits. This study used weighted gene co-expression network analysis (WGCNA) approach to (1) detect modules or clusters of differentially expressed genes (DEG) with similar expression patterns in calf rumen transcriptome during pre- and post-weaning periods and (2) identify regulatory mechanisms linking gene modules to relevant phenotypes during the pre-weaning period (day 33 [d33]): weight gain (BWT_d33), average daily gain (ADG_d33), blood glucose (Glucose_d33) and β-hydroxybutyrate (BHB_d33) concentrations and post-weaning period (d96): weight gain (BWT_d96), average daily gain (ADG_d96), blood glucose (Glucose_d96) and β-hydroxybutyrate (BHB_d96) concentrations, dry matter intake (DMI_d96) and feed efficiency (FE_d96). Rumen tissues were collected from 16 calves on d33 and another 16 on d96 for whole transcriptome sequencing ...
TY - JOUR. T1 - Gene expression profiling on lung cancer outcome prediction. T2 - Present clinical value and future premise. AU - Sun, Zhifu. AU - Yang, Ping. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2006/11. Y1 - 2006/11. N2 - DNA microarray has been widely used in cancer research to better predict clinical outcomes and potentially improve patient management. The new approach provides accurate tumor classification and outcome predictions, such as tumor stage, metastatic status, and patient survival, and offers some hope for individualized medicine. However, growing evidence suggests that gene-based prediction is not stable and little is known about the prediction power of gene expression profiles compared with well-known clinical and pathologic predictors. This review summarized up-to-date publications in microarray-based lung cancer clinical outcome prediction and conducted secondary analyses for those with sufficient sample sizes and associated clinical ...
Cervical cancer is the most common gynecologic malignant tumor, with a high incidence in 50-55-year-olds. This study aims to investigate the potential molecular mechanism of RRM2 for promoting the development of cervical cancer based on The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). RRM2 was found to be significant upregulated in cervical tissue (P,0.05) by extracting the expression of RRM2 from TCGA, GSE63514, GSE7410, GSE7803 and GSE9750. Survival analysis indicated that the overall survival was significantly worse in the patients with high-expression of RRM2 (P,0.05). The top 1000 positively/negatively correlated genes with RRM2 by Pearson Correlation test were extracted. The gene co-expression network by Weighted Gene Co-Expression Network Analysis (WGCNA) with these genes and the clinical characteristics (lymphocyte infiltration, monocyte infiltration, necrosis, neutrophil infiltration, the number of normal/stromal/tumor cells and the number of tumor nuclei) was ...
Background: Soft tissue sarcomas are heterogeneous and a major complication in their management is that the existing classification scheme is not definitive and is still evolving. Leiomyosarcomas, a major histologic category of soft tissue sarcomas, are malignant tumours displaying smooth muscle differentiation. Although defined as a single group, they exhibit a wide range of clinical behaviour. We aimed to carry out molecular classification to identify new molecular subgroups with clinical relevance. Methods: We used gene expression profiling on 20 extra-uterine leiomyosarcomas and cross-study analyses for molecular classification of leiomyosarcomas. Clinical significance of the subgroupings was investigated. Results: We have identified two distinct molecular subgroups of leiomyosarcomas. One group was characterised by high expression of 26 genes that included many genes from the sub-classification gene cluster proposed by Nielsen et al. These sub-classification genes include genes that have ...
A DNA microarray is a solid support such as a glass slide, silicon chip or nylon membrane on which DNA molecules are attached at precise locations. Using DNA microarrays, the expression of tens of thousands of genes in a biological sample can be detected in one experiment. Emerging data suggests that the use of DNA microarrays can aid the differentiation of tumors with similar morphological appearance, predict patient outcome independently of conventional prognostic factors and select for response or resistance to specific anti-cancer therapies. DNA microarray technology thus has the potential to supplement standard diagnostic procedures in oncology and permit a more individualized approach to patient management. Prior to clinical application, however, this methodology must be simplified, standardized, evaluated in external quality assessment schemes and made available at relatively low costs. Most importantly, the preliminary, but promising, early findings must be validated by high-level ...
TY - JOUR. T1 - Homogeneous datasets of triple negative breast cancers enable the identification of novel prognostic and predictive signatures. AU - Karn, Thomas. AU - Pusztai, Lajos. AU - Holtrich, Uwe. AU - Iwamoto, Takayuki. AU - Shiang, Christine Y.. AU - Schmidt, Marcus. AU - Müller, Volkmar. AU - Solbach, Christine. AU - Gaetje, Regine. AU - Hanker, Lars. AU - Ahr, Andre. AU - Liedtke, Cornelia. AU - Ruckhäberle, Eugen. AU - Kaufmann, Manfred. AU - Rody, Achim. PY - 2011/12/29. Y1 - 2011/12/29. N2 - Background: Current prognostic gene signatures for breast cancer mainly reflect proliferation status and have limited value in triple-negative (TNBC) cancers. The identification of prognostic signatures from TNBC cohorts was limited in the past due to small sample sizes. Methodology/Principal Findings: We assembled all currently publically available TNBC gene expression datasets generated on Affymetrix gene chips. Inter-laboratory variation was minimized by filtering methods for both samples ...
Table_6_Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum.XLSX
RNA Transcription Detected on Chromosomes 21 and 22 Using High Density Oligonucleotide Arrays. Thomas R. Gingeras, Affymetrix Inc., Santa Clara, CA. The first drafts of complete human genome sequence have brought with them the opportunities to map the RNA transcription patterns that are characteristic of each differentiated and undifferentiated cell type and characterize the sequence variations that underlie the phenotypic differences observed in the human population. By using the very high information content inherent in high-density oligonucleotide arrays it will be possible to map the locations of RNA transcription along the length of the entire human genome. Such a transcriptome map will provide information concerning: 1) the identification of novel transcription domains of the genome, 2) the predominant utilization of exon sequences during differentially spliced gene expression and 3) a empirically derived set of results which can be compared to the sequence annotation now being assembled ...
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation - Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time series gene expression following system perturbation: 1) Conditional, Tamoxifen dependent, activation of the cMyc proto-oncogene in rat fibroblast; 2) Genomic response to nutrition changes in D. melanogaster; 3) Patterns of gene activity as a consequence of ageing occurring over a life-span time series (25y-90y) sampled from T-cells of human donors. We show that the three datasets undergo similar transitions from an uncorrelated regime to a positively or negatively correlated one that is symptomatic of a shift from a ground or basal state to a polarized state. In
An award for difficult RNA samples. Gene expression profiling using Next Generation Sequencing (NGS) is empowering an ever-increasing range of researchers to answer highly relevant biological and medical questions. At Lexogen, we are dedicated to developing innovative technologies for NGS and making these accessible for all scientists. With the Lexogen Research Award we wish to provide a chance for researchers to utilize more NGS. We ask you to submit a description of the project where you would use NGS and Lexogens RNA-Seq sample prep. The winners shall be given a product of Lexogen together with a free sequencing run and data analysis. The topic of this Research Award is High quality from low quality: Accurate gene expression profiling of low quality or FFPE samples. RNA sequencing is rapidly becoming the platform of choice for gene expression profiling projects. However, not all samples are created equal, and not all researchers have the luxury of working with high quality RNA for NGS library
Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M. lutarioriparius with an emphasis to identify putative genes involved in rhizome development. Approximately 66 gigabase (GB) paired-end clean reads were obtained and assembled into 169,064 unigenes with an average length of 759 bp. Among these unigenes, 103,899 (61.5%) were annotated in seven public protein databases. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218 and 1,077 genes were predominantly expressed in root, leaf, stem, lateral bud, and rhizome bud, respectively. Their expression patterns were further classified into 12 distinct
The aims of the present study were to identify key genes and pathways associated with hepatocellular carcinoma (HCC) progression and predict compounds potentially associated with this type of carcinogenesis. The gene expression profile data of the GSE49515 dataset was obtained from the Gene Expression Omnibus database. The limma software package was used to identify the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Biological Networks Gene Ontology tool and the Database for Annotation, Visualization and Integrated Discovery, respectively. The Michigan Molecular Interactions database plugin within the Cytoscape software platform was used to perform protein‑protein interaction (PPI) network analysis. Chemical‑gene interaction data for HCC were obtained from the Comparative Toxicogenomics Database to evaluate the associations between drugs and specific genes. A total of 302 DEGs, including ...
Gene expression in multiple individual cells from a tissue or culture sample varies according to cell-cycle, genetic, epigenetic and stochastic differences between the cells. However, single-cell differences have been largely neglected in the analysis of the functional consequences of genetic variation. Here we measure the expression of 92 genes affected by Wnt signaling in 1,440 single cells from 15 individuals to associate single-nucleotide polymorphisms (SNPs) with gene-expression phenotypes, while accounting for stochastic and cell-cycle differences between cells. We provide evidence that many heritable variations in gene function--such as burst size, burst frequency, cell cycle-specific expression and expression correlation/noise between cells--are masked when expression is averaged over many cells. Our results demonstrate how single-cell analyses provide insights into the mechanistic and network effects of genetic variability, with improved statistical power to model these effects on gene
The transcription factor c-Myb is required for modulation of progenitor cells in several tissues, including skeletal muscle and its upregulation is observed in many human being malignancies. in RMS sufferers. c-Myb could, therefore, lead to the growth phenotype by performing its inhibitory function in skeletal muscles difference. We also demonstrated that c-Myb proteins is normally abundant in migratory C2C12 myoblasts and its ectopic reflection potentiates cell motility. In overview, our outcomes implicate that metastatic properties of some RMS subtypes might end up being linked to c-Myb function. The transcription aspect c-Myb is normally needed for the regulations of progenitor cells in many tissue, including the hematopoietic program1,2, the adult human brain3, and colonic crypts4. It has a function in progenitor creation, keeping their expansion, migration, or family tree dedication. c-Myb appearance generally diminishes as progenitor cells differentiate. In truth, constitutive ...
Osaka-Dental-University-Susceptible rats (ODUS/Odu) are a useful animal model for human periodontal disease. Through comprehensive gene expression profiling, we aimed to evaluate the utility of ODUS/Odu-derived cells as an alternative to animal models for biomedical research into human periodontal disease. Using a GeneChip Rat Expression Array containing 15923 probes, the gene expression profiles of embryonic fibroblasts obtained from 13.5-day-old embryos of ODUS/Odu or control rats were comprehensively analyzed. This profiling revealed alterations in some genes that are likely to be related to periodontal disease in ODUS/Odu, based on a comparison with genes found in databases. Osteopontin (OPN), which is involved in immune defense reactions, bone metabolism and chronic inflammation, was among the genes whose expressions were significantly altered. Realtime RT-PCR analysis showed that the OPN mRNA level was increased by more than 5.8-fold in ODUS/Odu. Moreover, the expression of CD44, a ...
Autologous hematopoietic stem cell transplantation (aHSCT) has been used as a therapeutic approach in multiple sclerosis (MS). However, it is still unclear if the immune system that emerges from autologous CD34+ hematopoietic progenitor cells (HPC) of MS patients is pre-conditioned to re-develop the proinflammatory phenotype. The objective of this article is to compare the whole genome gene and microRNA expression signature in CD34+ HPC of MS patients and healthy donors (HD). CD34+ HPC were isolated from peripheral blood of eight MS patients and five HD and analyzed by whole genome gene expression and microRNA expression microarray. Among the differentially expressed genes (DEGs) only TNNT1 reached statistical significance (logFC=3.1, p,0.01). The microRNA expression was not significantly different between MS patients and HD. We did not find significant alterations of gene expression or microRNA profiles in CD34+ HPCs of MS patients. Our results support the use of aHSCT for treatment of MS. ...
The epithelial to mesenchymal transition (EMT) plays a key role in lung cancer progression and drug resistance. The dynamics and stability of gene expression patterns as cancer cells transition from E to M at a systems level and relevance to patient outcomes are unknown. Using comparative network and clustering analysis, we systematically analyzed time-series gene expression data from lung cancer cell lines H358 and A549 that were induced to undergo EMT. We also predicted the putative regulatory networks controlling EMT expression dynamics, especially for the EMT-dynamic genes and related these patterns to patient outcomes using data from TCGA. Example EMT hub regulatory genes were validated using RNAi. We identified several novel genes distinct from the static states of E or M that exhibited temporal expression patterns or periods during the EMT process that were shared in different lung cancer cell lines. For example, cell cycle and metabolic genes were found to be similarly down-regulated where
TY - JOUR. T1 - A Sequence Based Validation of Gene Expression Microarray Data. AU - Thallinger, Gerhard. AU - Obermayr, Eva. AU - Charoentong, Pornpimol. AU - Tong, Dan. AU - Trajanoski, Zlatko. AU - Zeillinger, Robert. PY - 2012. Y1 - 2012. UR - http://thescipub.com/ajb.toc. U2 - 10.3844/ajbsp.2012.1.9. DO - 10.3844/ajbsp.2012.1.9. M3 - Article. VL - 1. SP - 1. EP - 9. JO - American journal of bioinformatics. JF - American journal of bioinformatics. SN - 1948-9862. IS - 1. ER - ...
Early detection of breast cancer is key to successful treatment and patient survival. We have previously reported the potential use of gene expression profiling of peripheral blood cells for early detection of breast cancer. The aim of the present study was to refine these findings using a larger sample size and a commercially available microarray platform. Blood samples were collected from 121 females referred for diagnostic mammography following an initial suspicious screening mammogram. Diagnostic work-up revealed that 67 of these women had breast cancer while 54 had no malignant disease. Additionally, nine samples from six healthy female controls were included. Gene expression analyses were conducted using high density oligonucleotide microarrays. Partial Least Squares Regression (PLSR) was used for model building while a leave-one-out (LOO) double cross validation approach was used to identify predictors and estimate their prediction efficiency. A set of 738 probes that discriminated breast cancer
Temperature adaptation is one of the most important determinants of distribution and population size of organisms in nature. Recently, quantitative trait loci (QTL) mapping and gene expression profiling approaches have been used for detecting candidate genes for heat resistance. However, the resolution of QTL mapping is not high enough to examine the individual effects of various genes in each QTL. Heat stress-responsive genes, characterized by gene expression profiling studies, are not necessarily responsible for heat resistance. Some of these genes may be regulated in association with the heat stress response of other genes. To evaluate which heat-responsive genes are potential candidates for heat resistance with higher resolution than previous QTL mapping studies, we performed genome-wide deficiency screen for QTL for heat resistance. We screened 439 isogenic deficiency strains from the DrosDel project, covering 65.6% of the Drosophila melanogaster genome in order to map QTL for thermal resistance.
Developmental Anatomic Gene Expression Atlas (AGEA) The Allen Gene Expression Atlas (AGEA) for the Developing Mouse Brain is used to understand how voxels of the brain are related by gene expression (Correlation), and to find genes expressed at a particul
PubMed Central Canada (PMC Canada) provides free access to a stable and permanent online digital archive of full-text, peer-reviewed health and life sciences research publications. It builds on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature and is a member of the broader PMC International (PMCI) network of e-repositories.
Purpose. human TM cells morphologically and started to specific many guns of TM cells while ceasing to specific pluripotency guns such as Nanog, April4, and Sox2. Functionally, the ability was created by these cells to phagocytose particles. Finally, publicity to dexamethasone or phorbol 12-myristate acetate triggered a specific boost in the creation and release of myocilin and matrix metalloproteinase-3, respectively, behavior quality of TM cells. Results. Our data show that iPSCs can be induced to assume a phenotype that resembles native TM cells in many important aspects. Not only do these cells represent a valuable research tool, but transplantation into glaucomatous eyes with elevated IOP may also restore function to the TM, resulting in re-establishment of IOP. … In order to induce iPSCs to differentiate into TM-like cells, iPSCs were cocultured with the human cell line hTM530 for up to 21 days. This immortalized cell line was used here since it grows at a very consistent rate and ...
Objective: To determine whether peripheral blood gene expression of patients with systemic lupus erythaematosus (SLE) correlates with disease activity measured using the SLE Disease Activity Index 2000 (SLEDAI-2K).. Methods: RNA was isolated from peripheral blood of 269 patients with SLE and profiled on a custom microarray. Hierarchical clustering and a heat map were used to categorise samples into major clusters based on gene expression pattern. Correlates, including demographic and disease-related characteristics such as SLEDAI-2K score, of the major sample clusters were compared using multivariate regression models.. Results: A set of 31 interferon (IFN)-regulated genes were seen to be driving the separations of samples into two clusters, one characterised by a relatively high IFN-regulated gene signature (n = 150) and the other by a relatively low IFN-regulated gene signature (n = 119). Disease activity measured using the SLEDAI-2K was significantly correlated with the high IFN gene ...
Gene expression network analysis and applications to immunology - We address the problem of using expression data and prior biological knowledge to identify differentially expressed pathways or groups of genes. Following an idea of Ideker et al. (2002), we construct a gene interaction network and search for high-scoring subnetworks. We make several improvements in terms of scoring functions and algorithms, resulting in higher speed and accuracy and easier biological interpretation. We also assign significance levels to our results, adjusted for multiple testing. Our methods are succesfully applied to three human microarray data sets, related to cancer and the immune system, retrieving several known and potential pathways. The method, denoted by the acronym GXNA (Gene eXpression Network Analysis) is implemented in software that is publicly available and can be used on virtually any microarray data set.
contribute to the vascular remodeling process associated with hypertension and atherosclerosis, the aims of this study were to assess the impact of 2-ME on pathophysiological pathways regulating SMC growth using transcriptional profiling. High-density oligonucleotide microarrays (Affymetrix Human Genome U_133 Plus 2.0 GeneChips) were used to identify differentially expressed genes in cultured human aortic SMCs treated with 2-ME (acutely, for 4 hrs, n=3; and chronically, for 48 hrs, n=3) and vehicle-treated time-matched controls (n=3 for each time point). Both single gene analysis (performed using Significance Analysis of Microarrays) as well as Gene Set Enrichment Analysis (GSEA, a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states) indicated downregulation of genes critically involved in mitotic spindle assembly and function in SMCs chronically treated with 2-ME when compared to ...
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.. Availability: Genoscape is an open-source software freely available from the Genoscape webpage (http://www.pasteur.fr/recherche/unites/Gim/genoscape/). Installation instructions and tutorial can also be found at this URL.. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.. ...
Purpose: To identify the novel gene signatures and molecular markers of nasopharyngeal carcinoma (NPC) by integrated bioinformatics analysis of multiple gene expression profiling datasets. Experimental Design: Seven published gene expression profiling studies and one of our unpublished works were reanalyzed to identify the common significantly dysregulated (CSD) genes in NPC. Overrepresentation analysis of cytogenetic bands, Gene Ontology (GO) categories, pathways were used to explore CSD genes functionally associated with carcinogenesis. The protein expressions of selected CSD genes were examined by immunohistochemistry on tissue microarrays, and the correlations of their expressions with clinical outcomes were evaluated. Results: Using the criteria (genes reported deregulated in more than one study), a total of 962 genes were identified as the CSD genes in NPC. Four up-regulated (BUB1B, CCND2, CENPF and MAD2L1) and two down-regulated (LTF and SLPI) genes were markedly reported in six studies. ...
Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages. We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes
TY - JOUR. T1 - MicroRNA expression profiling and Notch1 and Notch2 expression in minimal deviation adenocarcinoma of uterine cervix. AU - The Gynecological Pathology Study Group of the Korean Society of Pathologists. AU - Lee, Heejeong. AU - Kim, Kyu Rae. AU - Cho, Nam Hoon. AU - Hong, Sung Ran. AU - Jeong, Hoiseon. AU - Kwon, Sun Young. AU - Park, Kwang Hwa. AU - An, Hee Jung. AU - Kim, Tae Heon. AU - Kim, Insun. AU - Yoon, Hye Kyoung. AU - Suh, Kwang Sun. AU - Min, Ki Ouk. AU - Choi, Hyun Joo. AU - Park, Ji Young. AU - Yoo, Chong Woo. AU - Lee, Youn Soo. AU - Lee, Hee Jin. AU - Lee, Weon Sun. AU - Park, Chul Soo. AU - Lee, Yonghee. PY - 2014. Y1 - 2014. N2 - Background: MicroRNA (miRNA) expression is known to be deregulated in cervical carcinomas. However, no data is available about the miRNA expression pattern for the minimal deviation adenocarcinoma (MDA) of uterine cervix. We sought to detect deregulated miRNAs in MDA in an attempt to find the most dependable miRNA or their combinations to ...
This introductory course on microarray analysis is targeted to people without previous knowledge on this field. We will cover the basic steps that should be followed to obtain a list of differentially expressed genes, starting from raw expression data. The theoretical part of the course will be comprehensive and the similarities and differences between one- and two-color arrays will be discussed. For the practical part, an already published public dataset of Agilent two-color arrays will be used for all subsequent hands-on work. Students will get familiar with raw data format, background subtraction and normalization procedures that are needed before any differential expression analysis ...
Purpose: Minimal residual disease (MRD) presents a significant hurdle to curing metastatic neuroblastoma. Biological therapies directed against MRD can improve outcome. Evaluating treatment efficacy requires MRD measurement, which serves as surrogate endpoint. Because of tumor heterogeneity, no single marker will likely be adequate. Genome-wide expression profiling can uncover potential MRD markers differentially expressed in tumors over normal marrow/blood.. Experimental Design: Gene expression array was carried out on 48 stage 4 tumors and 9 remission marrows using the Affymetrix U95 gene chip. Thirty-four genes with a tumor-to-marrow expression ratio higher than tyrosine hydroxylase were identified. Quantitative reverse transcription-PCR was done on all 34 genes to study the dynamic range of tumor cell detection and the expression of these genes in normal marrow/blood samples and in stage 4 neuroblastoma tumors. Top ranking markers were then tested for prognostic significance in the marrows ...
(PRN) Quest Diagnostics Launches Test to Help Oncologists Predict Risk of Breast Cancer Recurrence in Women with Estrogen Receptor (ER)-Positive, Lymph Node- Negative Cancers IL17BR, to help physicians predict the risk of disease recurrence in women with estrogen receptor (ER)-positive, lymph node-negative breast cancer. Quest Diagnostics is the first company to develop a breast cancer recurrence test based on licensed gene-expression profiling technology from AviaraDx Inc., a molecular cancer profiling company located in Carlsbad, California. Launched at the San Antonio Breast Cancer Symposium, December 14 - 17, 2006, the Breast Cancer Gene Expression Ratio is based on the ratio of the expression of two genes: the homeobox gene-B13 (HOXB13) and the interleukin- 17B receptor gene (IL17BR). The clinical value of the Breast Cancer Gene Expression Ratio also is supported by a study published earlier this year in Clinical Cancer Research(2). According to the American Cancer Society (ACS), more than 210
A free online platform is being developed that uses a crowdsourcing approach to make public gene expression data more accessible to biomedical researchers.
To evaluate DNA methylation sites and gene expression associated with coronary artery disease (CAD) and the possible pathological mechanism involved, we performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood datasets from the Gene Expression Omnibus repository of CAD samples and controls; (2) functional enrichment analysis and differential methylation gene regulatory network construction; (3) validation tests of 11 differential methylation positions of interest and the corresponding gene expression; and (4) correlation analysis for DNA methylation and mRNA expression data. A total of 669 differentially expressed mRNAs were matched to differentially methylated genes. After disease ontology, Kyoto Encyclopedia of Genes and Genomes pathway, gene ontology, protein-protein interaction and network construction and module analyses, 11 differentially methylated positions (DMPs) corresponding to 11 unique genes were observed: BDNF - cg26949694, BTRC - cg24381155
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated ...
Looking for online definition of differential gene expression in the Medical Dictionary? differential gene expression explanation free. What is differential gene expression? Meaning of differential gene expression medical term. What does differential gene expression mean?
Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped that this review will give the readers a good understanding of the current development in this field and inspire them to come up with the next generation of imputation algorithms ...
In a variety of solid cancers, missense mutations in the well-established TP53 tumour suppressor gene may lead to presence of a partially-functioning protein molecule, whereas mutations affecting the protein encoding reading frame, often referred to as null mutations, result in the absence of p53 protein. Both types of mutations have been observed in the same cancer type. As the resulting tumour biology may be quite different between these two groups, we used RNA-sequencing data from The Cancer Genome Atlas (TCGA) from four different cancers with poor prognosis, namely ovarian, breast, lung and skin cancers, to compare the patterns of co-expression of genes in tumours grouped according to their TP53 missense or null mutation status. We used Weighted Gene Coexpression Network analysis (WGCNA) and a new test statistic built on differences between groups in the measures of gene connectivity. For each cancer, our analysis identified a set of genes showing differential coexpression patterns between the
MicroRNAs (miRNAs) finely tune messenger RNA (mRNA) expression. As the brain is a highly heterogeneous tissue, physiologically relevant miRNA expression profiling greatly benefits from sampling brain regions or nuclei. MiRNA expression profiling from individual samples is also important for investigating potential differences between animals according to their physiological and pathophysiological status[1].. [1] L.Amar et al., MicroRNA expressionprofiling of hypothalamic arcuate andparaventricular nuclei from single rats using Illumina sequencing technology;Journal of Neuroscience Methods;http://dx.doi.org/10.1016/j.jneumeth.2012.05.033. ...
"Global functional profiling of gene expression☆☆This work was funded in part by a Sun Microsystems grant awarded to S.D., NIH ... "Profiling Gene Expression Using Onto-Express". Genomics. 79 (2): 266-270. doi:10.1006/geno.2002.6698. Drǎghici, Sorin; Khatri, ... "Down-weighting overlapping genes improves gene set analysis". BMC Bioinformatics. 13 (1): 136. doi:10.1186/1471-2105-13-136. ... "A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures". Frontiers in Genetics. 10: ...
February 2002). "Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling ... Torres, TT; Metta, M; Ottenwälder, B; Schlötterer, C (January 2008). "Gene expression profiling by massively parallel ... The level of unique gene expression is represented by the count of transcripts present per million molecules, similar to SAGE ... 2000). "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays". Nature Biotechnology. ...
D. Geman; C. d'Avignon; D. Naiman; R. Winslow (2004). "Classifying gene expression profiles from pairwise mRNA comparisons". ... "Simple decision rules for classifying human cancers from gene expression profiles". Bioinformatics. 21 (20): 3896-3904. doi: ...
June 2003). "Expression profiling reveals off-target gene regulation by RNAi". Nature Biotechnology. 21 (6): 635-7. doi:10.1038 ... Herndon MK, Quirk CC, Nilson JH (January 2016). "Chapter 2 - Control of Hormone Gene Expression". In Jameson JL, De Groot LJ, ... If siRNA is able to successfully reach its target, it has the potential to therapeutically regulate gene expression through its ... So far, applications of antisense RNAs in antivirus and anticancer treatments and in regulating the expression of related genes ...
"Gene expression profiling of primary cutaneous melanoma and clinical outcome". Journal of the National Cancer Institute. 98 (7 ... Various different genes have been identified for both α and β, with some of them listed below. Note that often karyopherin and ... Since these initial discoveries in 1994 and 1995, a host of Importin genes, such as IPO4 and IPO7, have been found that ... As a result, a disruption in the expression patterns of importin-α has been shown to cause fertility defects in Drosophila ...
It shows tissue-enriched gene (TEG) expression when compared to housekeeping gene (HKG) expression. Its highest expression is ... ". "EST profile: TMEM261". UniGene. National Library of Medicine. Wu J, et al. (2012). "Identification and functional analysis ... "GeneCards:MEF2C Gene". Welch JJ, et al. (2004). "Global regulation of erythroid gene expression by transcription factor GATA-1 ... 2011). "Global gene expression analysis of human erythroid progenitors". Blood. 117 (13): e96-108. doi:10.1182/blood-2010-07- ...
"MicroRNA gene expression profile of hepatitis C virus-associated hepatocellular carcinoma". Hepatology. 47 (4): 1223-32. doi: ... MicroRNAs function to regulate the expression levels of other genes by several mechanisms. MicroRNA Lu J, Kwan BC, Lai FM, Tam ... Sung TL, Rice AP (January 2009). Hope TJ (ed.). "miR-198 inhibits HIV-1 gene expression and replication in monocytes and its ... Carter CJ (November 2009). "Schizophrenia susceptibility genes directly implicated in the life cycles of pathogens: ...
Fan, Jinhong; Ngai, John (2001). "Onset of Odorant Receptor Gene Expression during Olfactory Sensory Neuron Regeneration". ... The difference in affinities causes differences in activation patterns resulting in unique odorant profiles. The activated OR ... There are approximately 1000 different genes that code for the ORs, making them the largest gene family. An odorant will ... Bieri, S.; Monastyrskaia, K; Schilling, B (2004). "Olfactory Receptor Neuron Profiling using Sandalwood Odorants". Chemical ...
Comparison of gene expression profiles between human and mouse monocyte subsets. Blood, 115(3):e10-19. PMCID: PMC2810986 Tacke ... "Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue ... Gene expression profiles and transcriptional regulatory pathways underlying murine tissue macrophage identity and diversity. ... She spearheaded early work on mouse macrophage gene expression, and her paper published as a part of the Immgen Project is the ...
"The differentiation and gene expression profile of human dental follicle cells". Stem Cells and Development. 19 (5): 707-17. ... To find the reason between these differences, the genome-wide expression profiles were compared at an early differentiation ... Moreover, information about genome-wide expression profiles was provided by proteomics and transcriptomics with DFCs. These ... When stimulating alveolar bone growth at the base of the crypt, expression of the bone morphogenetic protein-6 in the dental ...
November 2005). "Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish". ... a decrease in the expression of genes involved in aerobic metabolism and an increase in expression of genes involved in ... Ton, C; Stamatiou, D; Liew, CC (April 2003). "Gene expression profile of zebrafish exposed to hypoxia during development". ... "Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis". Proc Natl Acad Sci USA. 98 (4): 1993- ...
1999). "Gene Expression Analysis by Transcript Profiling Coupled to a Gene Database Query". Nat. Biotechnol. 17 (8): 798-803. ... Gene Expression Analysis by Transcript Profiling Coupled to a Gene Database Query. Nature Biotechnology 17, 798-803: 1999 ... which are correlated with gene expression levels of specific transcripts. Differences between gene expression in healthy ... Expression Profiling of the Maize Flavonoid Pathway Genes Controlled by Estradiol-Inducible Transcription Factors CRC and P. ...
2008). "Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile". Mol. Cancer. 7: 41. doi: ... There is a strong correlation between 1p/19q codeletion and the expression of proneural genes, suggesting that gliomas with a ... The gene products lost as a consequence of this codeletion may include mediators of resistance to genotoxic therapies. ... Oligodendrogliomas show only rarely mutations in the p53 gene, which is in contrast to other gliomas. Epidermal growth factor ...
2006). "Gene expression profiling in vLINCL CLN6-deficient fibroblasts: Insights into pathobiology". Biochim. Biophys. Acta. ... "Entrez Gene: CLN6 ceroid-lipofuscinosis, neuronal 6, late infantile, variant". Bajaj L, Sharma J, di Ronza A, Zhang P, Eblimit ... Ceroid-lipofuscinosis neuronal protein 6 is a protein that in humans is encoded by the CLN6 gene. The CLN6 protein is part of ... Wheeler RB, Sharp JD, Schultz RA, Joslin JM, Williams RE, Mole SE (Jan 2002). "The gene mutated in variant late-infantile ...
Tanaka S, Tatsumi K, Okubo K, Itoh K, Kawamoto S, Matsubara K, Amino N (Feb 2002). "Expression profile of active genes in the ... "Cloning and expression of an immunoglobulin superfamily gene (IGSF1) in Xq25". Genomics. 48 (2): 157-62. doi:10.1006/geno. ... Gene. 214 (1-2): 1-6. doi:10.1016/S0378-1119(98)00253-4. PMID 9729118. "Entrez Gene: IGSF1 immunoglobulin superfamily, member 1 ... The IGSF1 gene is also active in the brain and in the developing liver. It can also become reactivated in liver cancer ( ...
... comprehensive analysis of protein-protein interactions and gene expression profiling". BMC Genomics. 9: 220. doi:10.1186/1471- ... One such gene is Myc. The level of production of the different CPEB proteins determines whether the expression of Myc leads to ... The tumor suppressor gene TP53 has also been shown to be regulated by a CPE. Cell lines that do not produce CPEB show lower ... Chen, Yun; Tsai, Ya-Hui; Tseng, Sheng-Hong (2016-11-01). "Regulation of the Expression of Cytoplasmic Polyadenylation Element ...
... is a highly ubiquitously expressed gene that has shown expression in many tissues. "BLAT". UCSC Genome Bioinformatics. " ... "ARMCX5". Gene cards. "NCBI- nucleotide". "NCBI BLAST". "NCBI-protein". "NCBI-EST profiles".. ... ARMCX5 is an armadillo repeat-containing protein that is encoded by the X-linked ARMCX5 gene. It is conserved only in Eutheria ...
"An Eight-Gene Blood Expression Profile Predicts the Response to Infliximab in Rheumatoid Arthritis". PLOS ONE. 4 (10): e7556. ... "Gene Expression Profiling Reveals Distinct Molecular Signatures Associated With the Rupture of Intracranial Aneurysm". Stroke. ... It was found that in ruptured aneurysms, C11orf42 was ranked at 55.5% among other genes and had an expression level of 8.16. In ... "Gene: C11orf42 - ENSG00000180878". bgee.org. Retrieved 2019-02-26. "EST Profile - Hs.278221". www.ncbi.nlm.nih.gov. Nakaoka, ...
Chabot, J R; J. M. Pedraza; P. Luitel; A. van Oudenaarden (2007). "Stochastic gene expression out-of-steady-state in the ... Alex van Oudenaarden's Lab @ MIT Alex van Oudenaarden's faculty profile @ MIT. ... Today, Van Oudenaardens work at the Hubrecht Institute focuses on stochastic gene expression, developing new tools for ... "Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway". Cell. 155 (4): 869-880. doi:10.1016 ...
January 2013). "Expression of trisomic proteins in Down syndrome model systems". Gene. 512 (2): 219-225. doi:10.1016/j.gene. ... May 2013). "Protein profiles in Tc1 mice implicate novel pathway perturbations in the Down syndrome brain". Hum. Mol. Genet. 22 ...
He is known for his studies on the regulation of Gene expression and his contributions in cancer diagnostics and the ... "Brief Profile of the Awardee". Shanti Swarup Bhatnagar Prize. 2016. Retrieved 5 October 2016. "Fellow profile - T K Kundu". ... "Epigenetic Regulation of Chromatin Dynamics and Gene Expression: Implications in Differentiation, Disease and Therapeutics". ... "Epigenetic Regulation of Chromatin Dynamics and Gene Expression: Implications in Differentiation, Disease and Therapeutics" ( ...
"Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proc. Natl. Acad. Sci ... "Entrez Gene: ARPP-21 cyclic AMP-regulated phosphoprotein, 21 kD". CS1 maint: discouraged parameter (link) Human ARPP21 genome ... Brené S, Lindefors N, Ehrlich M, Taubes T, Horiuchi A, Kopp J, Hall H, Sedvall G, Greengard P, Persson H (1994). "Expression of ... Cyclic AMP-regulated phosphoprotein, 21 kD, also known as ARPP-21, is a human gene. GRCh38: Ensembl release 89: ENSG00000172995 ...
"Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proceedings of the ... It seems likely then, that this gene is a transcription factor, which regulates the expression of other genes important for the ... however its reported expression is 1.2 times that of the average gene. It has highest expression in the pancreas and nervous ... This gene was first identified in the hypothalamic-pituitary-adrenal axis (HPA axis). The GEO and EST profiles in NCBI, ...
"Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection ... A. parasiticus normally reproduces asexually however, the presence of single mating genes MAT1-1 or MAT1-2 in different strains ... "Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus". Fungal ...
digital atlas of gene expression patterns in the mouse Brito-Babapulle V, Catovsky D (August 1991). "Inversions and tandem ... "EST Profile - Hs.271614". EST Profile Viewer. National Center for Biotechnology Information (NCBI). "GENEPAINT Set ID: EH1992 ... None of this information gives any indication of a specific function but the wide expression of the gene and its high ... The homolog in mice also shows expression throughout the entire body. Several micro-arrays demonstrate the variable expression ...
Rapid Assessment of Clinical Grade Dendritic Cells by Gene Expression Profiling". Molecular Therapy. 21 (2): 476-484. doi: ... NIH Information Page Speaker Biography, NIH Demystifying Medicine Series (2007) NCI Spotlight on Scientists Profile (video). ...
Zhang XHD (2009). "A method for effectively comparing gene effects in multiple conditions in RNAi and expression-profiling ... With the dual-flashlight plot, we can see how the genes or compounds are distributed into each category in effect sizes, as ... Zhang XHD (2010). "Assessing the size of gene or RNAi effects in multifactor high-throughput experiments". Pharmacogenomics. 11 ... genes, et al.) with a desired size of inhibition or activation effects. A compound with a desired size of effects in an HTS ...
MicroRNAs function to regulate the expression levels of other genes by several mechanisms. MicroRNA Nam EJ, Lee M, Yim GW, Kim ... JH, Kim S, Kim SW, Kim YT (May 2012). "MicroRNA profiling of a CD133(+) spheroid-forming subpopulation of the OVCAR3 human ...
MicroRNAs function to regulate the expression levels of other genes by several mechanisms. miR-451 regulates the drug- ... This is made possible by different miRNA profiles of miRNAs in the different tissue types. van Jaarsveld, MT; Helleman, J; ... Page for mir-451 microRNA precursor family at Rfam "MicroRNA MIR451 family (MIR451) Gene group". HUGO Gene Nomenclature ... Svasti S, Masaki S, Penglong T, Abe Y, Winichagoon P, Fucharoen S, Umemura T (2010). "Expression of microRNA-451 in normal and ...
"Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans". Cell. 139 (3): 623-633. doi:10.1016/j.cell. ...
... appearance-observable traits caused by the expression of a condition's genes. The features of craniosynostosis' particular ... defining a syndrome-specific risk profile". Journal of Plastic, Reconstructive & Aesthetic Surgery. 63 (10): 1635-41. doi: ... in FGFR genes) and mutations that lead to loss of function (in TWIST genes).[38][39] Craniosynostosis is therefore likely the ... Gene Loeys-Dietz syndrome wide-set eyes • split uvula or cleft palate • arterial tortuosity • aortic root dilatation • ...
... classical QTL analyses were combined with gene expression profiling i.e. by DNA microarrays. Such expression QTLs (eQTLs) ... Several genes factor into determining a person's natural skin color, so modifying only one of those genes can change skin color ... The DNA sequence of any genes in this region can then be compared to a database of DNA for genes whose function is already ... It may indicate that plant height is controlled by many genes of small effect, or by a few genes of large effect. ...
2009). «Fibulin-4 regulates expression of the tropoelastin gene and consequent elastic-fibre formation by human fibroblasts». ... 2009). «Association of genetic variants with chronic kidney disease in individuals with different lipid profiles». Int. J. Mol ... Ontologia do gene. Função molecular. •extracellular matrix structural constituent. •protein binding. •extracellular matrix ... Rosenbloom J (1984). «Elastin: relation of protein and gene structure to disease». Lab. Invest. 51 (6): 605-23. PMID 6150137. ...
Early examples of artistic expression, such as the Venus of Tan-Tan and the patterns found on elephant bones from Bilzingsleben ... It is thought that wild foods can have a significantly different nutritional profile than cultivated foods.[117] The greater ... "Chimps, Humans 96 Percent the Same, Gene Study Finds". Retrieved 23 December 2013 ...
The video exploits Tilton's facial expressions and preaching style. The original video contained no title screen and was ... Some of Tilton's fundraising letters were written by Gene Ewing, who heads a multimillion-dollar marketing empire writing ... to the Trinity Foundation for help told him they had lost all of their money making donations to some of the higher profile ...
"Expression profile of active genes in human periodontal ligament and isolation of PLAP-1, a novel SLRP family gene". Gene. 275 ... "Expression pattern and gene characterization of asporin. a newly discovered member of the leucine-rich repeat protein family". ... "Entrez Gene: ASPN asporin". مؤرشف من الأصل في 05 ديسمبر 2010. الوسيط ,مسار أرشيف=. تم تجاهله (مساعدة); الوسيط ,تاريخ أرشيف=. تم ... Yamada S، Ozawa Y، Tomoeda M، Matoba R، Matsubara K، Murakami S (May 2006). "Regulation of PLAP-1 expression in periodontal ...
2002). "Regulated expression of the apolipoprotein E/C-I/C-IV/C-II gene cluster in murine and human macrophages. A critical ... "DNA sequence variation in human apolipoprotein C4 gene and its effect on plasma lipid profile". Atherosclerosis. 152 (1): 193- ... Apolipoprotein (apo)C4 gene is a member of the apolipoprotein C gene family. It is expressed in the liver and has a predicted ... Apo C4 is a 3.3-kb gene consisting of 3 exons and 2 introns; it is located 0.5 kb 5' to the APOC2 gene.[5] ...
Rush J، Moritz A، Lee KA، Guo A، Goss VL، Spek EJ، Zhang H، Zha XM، Polakiewicz RD، Comb MJ (2005). "Immunoaffinity profiling ... Miehe U، Kadyrov M، Neumaier-Wagner P، Bartz C، Rath W، Huppertz B (2007). "Expression of the actin stress fiber-associated ... Gene. 165 (2): 267-71. PMID 8522188. doi:10.1016/0378-1119(95)00542-E. .mw-parser-output cite.citation{font-style:inherit}.mw- ... Brill LM، Salomon AR، Ficarro SB، Mukherji M، Stettler-Gill M، Peters EC (2004). "Robust phosphoproteomic profiling of tyrosine ...
Such a gene that exhibits multiple phenotypic expression is called a pleiotropic gene . Therefore mutation in a pleiotropic ... "Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and ... One basic model of pleiotropy's origin describes a single gene locus to the expression of a certain trait. The locus affects ... Sickle cell anemia is a pleiotropic disease because the expression of a single mutated HBB gene produces numerous consequences ...
"Control of Gene Expression". The Medical Biochemistry Page (en inglés). Consultado o 19 de setembro de 2008.. ... "Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles" (PDF). Proceedings of the National ... Serial Analysis of Gene Expression, Análise en serie da expresión xénica), MPSS (Massively Parallel Signature Sequencing, ... "Anatomy of a Comparative Gene Expression Study" (en inglés). Washington University in St. Louis - Dpt. of Computer Science & ...
For example, increased maternal licking and grooming has been shown to alter expression of the glutocorticoid receptor gene ... Stressors that are uncontrollable, threaten physical integrity, or involve trauma tend to have a high, flat diurnal profile of ... de Kloet ER, Sibug RM, Helmerhorst FM, Schmidt MV, Schmidt M (April 2005). "Stress, genes and the mechanism of programming the ... Kim JE, Cho BK, Cho DH, Park HJ (July 2013). "Expression of hypothalamic-pituitary-adrenal axis in common skin diseases: ...
de Kloet, RS; de Kloet SR (2005). "The evolution of the spindlin gene in birds: Sequence analysis of an intron of the spindlin ... The verb "parrot" in the dictionary means "to repeat by rote". Also clichés such as the British expression "sick as a parrot" ... Measures taken to conserve the habitats of some high-profile charismatic species have also protected many of the less ... Conservation measures to conserve the habitats of some of the high-profile charismatic parrot species has also protected many ...
In budding yeast, the candidate gene for activation of histone gene expression is SBF. SBF is a transcription factor that is ... Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (May 2007). "High-resolution profiling of ... This affects their function of gene regulation. In general, genes that are active have less bound histone, while inactive genes ... NPAT activates histone gene expression only after it has been phosphorylated by the G1/S-Cdk cyclin E-Cdk2 in early S phase.[ ...
In 1988 Ed Harlow demonstrates that cancer-causing and cancer-preventing genes (oncogenes and tumor-suppressor genes) interact; ... 21] See the classic paper McClintock B 1951 "Chromosome Organization and Genic Expression" (Cold Spring Harbor Symp. Quant. ... In 2011, Wigler, James Hicks and Nick Navin perform the first genomic profile of single cancer cells from a patient's tumor;[42 ... The program began as an initiative of Eugene G. Blackford and Franklin Hooper, director of the Brooklyn Institute of Arts and ...
Their subsequent work shows how the SREBP pathway regulates expression of many genes that control lipid formation and ... sample taken after fasting is taken by a doctor or a home cholesterol monitoring device to determine a lipoprotein profile. ... of a number of genes to stimulate their transcription. Among the genes transcribed are the LDL receptor and HMG-CoA reductase. ...
Mohamed Adhikari (2004). "'Not Black Enough': Changing Expressions of Coloured Identity in Post-Apartheid South Africa" (PDF). ... a number of high-profile cases highlighted the legal and community attitude that identifying as Aboriginal or Torres Strait ... "Sex-biased gene flow in African Americans but not in American Caucasians", GMR, 2007, Vol. 12, No. 6. ...
2006). "Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma". Int. J. Cancer. 118 (5): 1165-72. doi: ... Güre AO, Wei IJ, Old LJ, Chen YT (2002). "The SSX gene family: characterization of 9 complete genes". Int. J. Cancer. 101 (5): ... 2003). "A novel fusion gene, SS18L1/SSX1, in synovial sarcoma". Genes Chromosomes Cancer. 37 (2): 195-200. doi:10.1002/gcc. ... This article on a gene on the human X chromosome and/or its associated protein is a stub. You can help Wikipedia by expanding ...
The genes expressions are mapped in a control sample to formulate a developmental chart of the gene expression at certain time ... Gene expression studies[edit]. Although physical characteristics and sizes at various instars have been used to estimate fly ... This is done by breaking the stages down into smaller units separated by predictable changed in gene expression.[33] Three ... This chart can then be compared to the measured values of gene expression to accurately predict the age of an egg to within two ...
profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. Search. ... "Gastric and intestinal phenotypes of gastric carcinoma with reference to expression of brain (fetal)-type glycogen ... More than 65 mutations in the PYGM gene that lead to McArdle disease have been identified to date.[15][16] Symptoms of McArdle ... in the glycogen phosphorylase gene in a patient with hepatic glycogen storage disease and residual enzyme activity". Molecular ...
"Interactive Drug Analysis Profile - Isotretinoin". mhra.gov.uk. Medicines & Healthcare Products Regulatory Agency. 31 March ... Isotretinoin is also thought to affect the serotonergic system - it increases expression of 5-HT1A receptors in the pre- ... schizophrenia and the retinoid cascade have been linked to the same gene loci;[47] and retinoid dysfunction causes congenital ... "Thyroid hormones and retinoids: a possible link between genes and environment in schizophrenia" (PDF). Brain Research Reviews ...
profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. Search. ... "SOD1 mRNA expression in sporadic amyotrophic lateral sclerosis". Neurobiology of Disease. 39 (2): 198-203. doi:10.1016/j.nbd. ... The genes are located on chromosomes 21, 6, and 4, respectively (21q22.1, 6q25.3 and 4p15.3-p15.1). ... but more than 5-fold in mutants deleted for either the SOD1 or SOD2 genes.[31] Reactive oxygen species levels increase with age ...
Gene expression profiling revealed the prevalence of specific fibroblast growth factors (FGFs) and FGF receptors in NSCLC cell ... Recent research revealed that IL-6 secretion induced by HER2 overexpression activated STAT3 and altered gene expression, ... In addition, expression of PDGFRα and -β correlated with invasive behavior in human mammary carcinomas. This indicates the ... It has been shown that phosphorylation of STAT3 and RANTES expression are increased in response to tamoxifen in human breast ...
... a potential biomarker identified by laser-capture microdissection-micro serial analysis of gene expression of human prostate ... Over-expression and ectopic expression of the protein may be associated with prostate adenocarcinoma.[3] ... Dicarbonyl/L-xylulose reductase, also known as carbonyl reductase II, is an enzyme that in human is encoded by the DCXR gene ... The DCXR gene encodes a membrane protein that is approximately 34 kDa in size and composed of 224 amino acids. The protein is ...
... mutations in other genes are rare.[1] People who have one abnormal copy (are heterozygous) of the LDLR gene may develop ... Class II: LDLR is not properly transported from the endoplasmic reticulum to the Golgi apparatus for expression on the cell ... and each are classified from both the altered lipid profile and by the genetic abnormality. For example, high LDL (often due to ... Abnormalities in the ARH gene, also known as LDLRAP1, were first reported in a family in 1973.[14] In contrast to the other ...
Palladino, Paolo (June 2002). "Review of The Century of the Gene by Evelyn Fox Keller". The British Journal for the History of ... "Photoinactivation and the Expression of Genetic Information in Bacteriophage-Lambda"[2] (1963). ... "Community of Scholars Profile". Institute for Advanced Study website. Institute for Advanced Study. Retrieved 16 February 2013. ... "Review of The Century of the Gene by Evelyn Fox Keller". Kirkus Reviews. 1 October 200.. ...
Eugene Paul Wigner; Andrew Szanton (1992). Andrew Szanton, ed. The Recollections of Eugene P. Wigner As Told to Andrew Szanton ... nor even with an expression of emotional antipathy, for he loved to use religious expressions and metaphors, but simply by ... Horgan, J. (1992) Profile: Hans A. Bethe - Illuminator of the Stars, Scientific American 267(4), 32-40. ... Eugene Dynkin (1924-2014): Soviet and American mathematician. He has made contributions to the fields of probability and ...
A high-profile recall in 2009-2010 involving Toyota vehicles with throttles that became stuck in the open position may have ... Homi J. Bhabha derived an expression for the probability of scattering positrons by electrons, a process now known as Bhabha ... Shielding Space Travelers by Eugene Parker.. *Anomalous cosmic ray hydrogen spectra from Voyager 1 and 2 ...
"Profile Books. Retrieved 6 December 2015.. *^ Hello Igor... Daniel Radcliffe gets into character on the set of the brand new ... Gene Wilder portrayed the descendant of Dr. Frankenstein (who insists on pronouncing it "Fronkonsteen"), with Peter Boyle as ... "the author's original genius and happy power of expression" (620), although he is less convinced about the way in which the ... 2012: An interactive ebook app created by Inkle and Profile Books that retells the story with added interactive elements.[69] ...
"Profiles in Science. United States National Library of Medicine. Archived from the original on May 5, 2009.. ... l-gulonolactone oxidase coding gene.[185] In 2008, researchers at the University of Montpellier discovered that in humans and ... so that enzyme expression peaks in the morning to support biosynthesis later on when mid-day sunlight intensity demands high ... Lachapelle, MY; Drouin, G (2010). "Inactivation dates of the human and guinea pig vitamin C genes". Genetica. 139 (2): 199-207 ...
Csóka AB, Scherer SW, Stern R (September 1999). "Expression analysis of six paralogous human hyaluronidase genes clustered on ... profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. Search. ... Elevated tissue expression of hyaluronic acid and hyaluronidase validates the HA-HAase urine test for bladder cancer.[14] ... Gene-targeting studies show that hyaluronidases such as PH20 are not essential for fertilization,[19] although exogenous ...
Gene expression profile: Any set of genes that are known to be expressed in a specific sample. Gene expression profiles can be ... Gene expression signature: A specific gene expression profile, often a subset of expressed genes usually associated with a ... DNA arrays are commonly used for gene expression profiling (that is, monitoring expression levels of thousands of genes ... We distinguished between gene expression signatures and the gene expression-based marketed tests. The gene signature is the ...
World Conference on Genotype Profiling & Gene Expressions. Future Conference: GENE EXPRESSION 2018; GENE EXPRESSION 2019; GENE ... GENE EXPRESSION 2017 - World Conference on Genotype Profiling & Gene Expressions. View: 181 ... Conference will explore the Genotype Profiling & Gene Expressions outlines and various ailments. Gene Expression 2017 is an ... Category Gene Expression events 2017; genetics conferences USA; Gene Expression conference; evolutionary biology conference; ...
Population-based analysis with Adjuvant! Online and genomic profiling with Oncotype DX are two commonly used tools in patients ... the population-based prognostic and predictive information differed dramatically from that obtained from genomic profiling and ... Schuster, S.R.; Pockaj, B.A.; Bothe, M.R.; David, P.S.; Northfelt, D.W. Clinical Utility of Gene Expression Profiling Data for ... Clinical Utility of Gene Expression Profiling Data for Clinical Decision-Making Regarding Adjuvant Therapy in Early Stage, Node ...
... liver disease and HCC gene expression profiles from public microarray data repositories ArrayExpress and Gene Expression ... 2009) Integration of ERG gene mapping and gene-expression profiling identifies distinct categories of human prostate cancer. ... Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker. Aileen Marshall,#1,2,* Margus ... Global gene expression profiling was performed for 4 normal (control) livers as well as 8 background liver and 7 HCC from 3 ...
... gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global ... Categorizing regulated genes[edit]. Having identified some set of regulated genes, the next step in expression profiling ... is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global ... Gene set analysis demonstrated several major advantages over individual gene differential expression analysis.[17][18] Gene ...
Gene expression (GE) analyses by use of microarrays (MAs) have become an important part of biomedical and clinical research and ... Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of ... Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med. 2004;350:1617-1628.CrossRefPubMedGoogle ... Gene expression profiling of pediatric acute myelogenous leukemia. Blood. 2004;104:3679-3687.CrossRefPubMedGoogle Scholar ...
Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Measurement of gene expression profiles in toxicity determination. US6479235. 25 Nov 1998. 12 Nov 2002. Promega Corporation. ... Methods and systems for dynamic gene expression profiling. WO2004048528A2. 21 Nov 2003. 10 Jun 2004. Primera Biosystems. ...
At the facility, researchers will use image analysis technology and molecular biology processes to generate gene expression ... Rosetta Inpharmatics inaugurated Thursday a new gene expression profiling facility in Bothell, Wash. ... NEW YORK, December 14 - Rosetta Inpharmatics inaugurated Thursday a new gene. expression profiling facility in Bothell, Wash.. ... Our new facility in Bothell will help us further our efforts in gene. expression research, and will advance our goal to develop ...
The phenotypic expression of these genes, through the synthesis of specific proteins, involves interaction with envi ... The genetic basis for disease is determined by the inheritance of genes containing specific sequences of deoxyribonucleic acid ... changes in gene expression take place that result in the expression of hundreds of gene products and the suppression of others ... Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U ...
Elucidation of β-Oxidation Pathways in Ralstonia eutropha H16 by Examination of Global Gene Expression Christopher J. Brigham, ... A Systems Biology Approach To Modeling Vibrio cholerae Gene Expression under Virulence-Inducing Conditions Sanjat Kanjilal, ... Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity Melanie J. ... GENE REGULATION. Transcriptomic and Phenotypic Characterization of a Bacillus subtilis Strain without Extracytoplasmic Function ...
Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. ... Expression profiling reveals off-target gene regulation by RNAi.. Jackson AL1, Bartz SR, Schelter J, Kobayashi SV, Burchard J, ... Transcript profiles revealed siRNA-specific rather than target-specific signatures, including direct silencing of nontargeted ... genes containing as few as eleven contiguous nucleotides of identity to the siRNA. These results demonstrate that siRNAs may ...
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... might be captured by profiling gene expression using DNA microarrays. Indeed, microarray profiling studies have identified ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer Message Subject (Your Name) has sent you a ...
Our study provides a comprehensive picture of the gene expression landscape in hepatocytes grown on different substrate ... 1370 genes that were up-regulated and 2677 down-regulated genes on stiff substrate. Functional enrichment analysis indicated ... Differentially expressed gene Hepatocyte RNA-sequencing Substrate stiffness Tingting Xia and Runze Zhao contributed equally to ... Email authorView authors OrcID profile. *1.Key Laboratory of Biorheological Science and Technology, Ministry of Education, ...
Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, and ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis Message Subject (Your Name) has sent you a ...
A gene expression-based recurrence predictor algorithm was informative in predicting the outcome in patients with early-stage ... We analyzed expression profiles of 12,625 transcripts in prostate tumors from patients with distinct clinical outcomes after ... Prostate tumor samples were taken from the patients at the time of surgery and subjected to a microarray gene expression ... PAIs defined by the expression profile of the prostate cancer recurrence predictor signature 1 for 21 prostate carcinoma ...
Tumor Gene Expression Profiling To Predict Risk of Breast Cancer Recurrence: EGAPP™ Recommendation.  alert icon ... Several gene expression profiles (GEPs) are clinically available that provide variations on "recurrence risk scores" intended ... The EGAPP™ Working Group examined the scientific evidence to see whether gene expression profiling is valid and useful for this ... Summary of Findings on Gene Expression Profiling To Predict Risk for Breast Cancer Recurrence. In 2009, the independent ...
Through gene expression profiling, UC Davis neuroscientists are discovering ways to monitor brain health and predict strokes, ... Gene Expression Profiling. Through gene expression profiling, researchers are working to find ways to monitor brain health and ... Using the latest microarray technology, researchers are creating gene expression profiles of people who have suffered strokes ... and other cerebrovascular disorders and comparing those to the gene expression profiles of healthy subjects and those who have ...
Gene expression data (GSE29801: NCBI, Geo) of macular and extramacular specimens of the retinas and retinal pigment epithelium ... Gene lists defined by cladogram nodes showed that the AMD-related deregulations occurring in the neural retina were different ... Gene lists from cladograms nodes were processed in Genomatix GePS to reveal the affected signaling pathway networks. ... Our analysis suggests a more complex transcriptional profile of the phenotypes than expected. Evaluation of the disease in much ...
... and gene expression profiling can be particularly helpful.. Several gene expression profiling tests exist, and many are being ... Gene expression profiling tests (Oncotype DX, MammaPrint, others) analyze a number of different genes within your cancer cells ... Ive heard that a gene expression profiling test might help in planning my treatment. What is it?. Answer From Sandhya Pruthi, ... The results of gene expression profiling tests help doctors determine who may benefit from additional (adjuvant) treatment ...
Gene Expression Profiling Shows Promise for CA Treatment. December 8th, 2005 Medgadget Editors News ... Using Tibshiranis approach they found 259 interesting genes. Whether these genes were being actively used by a particular ... He said the new tool he and his colleagues developed looks for larger groups of genes - equivalent to searching for pitchforks ... Brooks and Zhao analyzed the genes that were turned on or off in kidney tumors removed by their collaborators at Umea ...
Gene expression profiling studies of diffuse large B-cell lymphoma (DLBCL) have shown that this diagnostic category encompasses ... Gene expression profiling using DNA microarrays has great potential to improve the understanding, diagnosis, and management of ... Molecular diagnosis of lymphoid malignancies by gene expression profiling Curr Opin Hematol. 2002 Jul;9(4):333-8. doi: 10.1097/ ... Gene expression profiling studies of diffuse large B-cell lymphoma (DLBCL) have shown that this diagnostic category encompasses ...
Gene expression profile/profiling (GEP): The individual pattern of expression of a panel of genes that is regarded as a " ... Gene expression was examined using high-density oligonucleotide arrays. An analysis showed that gene expression profiling of ... class 2 gene expression profile signature and a negative SLNB result and individuals with a class 2 gene expression profile ... "gene expression profile class assignment of different sign for the tumor cells obtained from the two sites or a failed gene ...
Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR ... DNA databases and DNA profiling posted by the @ 3/12/2007 07:25:00 PM DNA databases and DNA profiling ...
QIAGEN offers a range of solutions for profiling pathogen gene expression. Our tools provide efficient mechanical disruption of ... For fast, one-step qRT-PCR using sequence-specific probes for gene expression analysis Show details ... Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ... Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ...
... J Transl Med. 2007 Feb 21;5:11. doi: 10.1186/1479-5876-5-11. ... Results: Four gene signatures whose expression changed relative to baseline (before wound induction by the pre-treatment biopsy ... The fourth and smallest set of genes was down-regulated throughout the study. Early in wound healing the expression of markers ... The largest group was comprised predominantly of inflammatory genes whose expression was increased throughout the study. Two ...
... the majority of cells within a tumor will share a common profile of gene expression. Gene expression profiling is a technique ... Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously ... gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression ... This allows for reliable identification of tumor type based on gene expression. A more powerful result of gene expression ...
Isolation of specific neurons from C. elegans larvae for gene expression profiling.. Spencer WC1, McWhirter R1, Miller T2, ... Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of ... Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling ... Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling ...
Breast cancer gene expression profiles (GEPs) look at the activity of genes within breast tumor tissue samples. Certain ... What is the purpose of the gene expression profiling test?. To predict the chance of the cancer recurring in the same or in ... General Public: Can Tumor Gene Expression Profiling (GEP) Improve Outcomes in Patients With Breast Cancer?.  alert icon ... Did EGAPP™ recommend using gene expression profiling to determine breast cancer recurrence risk? *No: The EGAPP™ Working Group ...
Other articles related to gene, gene expression, expression, expression profiling, gene expression profiling, genes:. ... Gene expression profiling In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are ... Gene Expression Profiling. In the field of molecular biology, gene expression profiling is the measurement of the activity (the ... Gene Expression Profiling - Conclusions. ... Expression profiling provides new information about what genes do under various ...
MN cells from five healthy donors were pulsed with SC and gene expression profiles of 18,861 genes were assessed in a micro- ... Gene expression profiling of suppressor mechanisms in tuberculosis. Journal. Molecular Immunology. Volume , Issue number. 45 , ... Twenty-eight genes were found to be increased and 60 genes were decreased (FDR = 1%, fold change , 1.4) in response to SC. ... This study (1) identifies the genes that modulate the T helper response, (2) describes their function, and (3) postulates a ...
Home -, Genomics -, Gene Expression Profiling Gene Expression Profiling. * Human Genome-wide Expression Profiling by Multiplex- ... Mouse Targeted Expression Profiling by Multiplex-RT PCR and subsequent NGS * Plate Based Gene Expression Profiling ( ... Human Targeted Expression Profiling by Multiplex-RT PCR and subsequent NGS * ... Next Generation Sequencing Protein Expression Transcription Factors Cell Signaling & Tracking Multiplex Cytokine Assays Gene ...
... Julie Anne Côté,1,2,3 Frédéric Guénard,3 ... To characterize changes in gene expression profile during human mature adipocyte dedifferentiation in ceiling culture. Methods ... Gene expression analysis at days 0, 4, 7, and 12 of the cultures was performed using Affymetrix Human Gene 2.0 STvi arrays. ... Four clusters gathered genes with similar expression between day 4 to day 7 but decreasing expression from day 7 to day 12. ...
... solutions for high-quality gene expression and transcriptome analysis and profiling studies. ... and high confidence mapping of alternate transcripts and gene fusions. Discover novel gene isoforms, profile gene expression ... Analyze Gene Expression in Single Cells. Highly sensitive RNA-Seq methods enable gene expression analysis of very low-input ... RNA-Seq for Gene Expression Analysis. Illumina offers a complete, accessible RNA-Seq workflow solution for gene expression and ...
  • Differentially expressed genes (DEGs) were computed based on gene expression profiles from GSE32018, GSE56315, and The Cancer Genome Atlas (TCGA) DLBC. (portlandpress.com)
  • The analysis of gene expression data can be broadly grouped into two categories: the identification of differentially expressed genes (or gene-sets) between two or more known conditions, and the unsupervised identification (clustering) of samples or genes that exhibit similar profiles across the data set. (biomedcentral.com)
  • Differentially-expressed genes related to cell traffic were selected and grouped into the clusters (i) matrix metallopeptidases, (ii) chemokines/chemokine receptors, and (iii) integrins. (biomedcentral.com)
  • Reproducibility, sensitivity and reliability in calling differentially expressed genes were evaluated by both Real-Time PCR and GeneChip® technology (Affymetrix). (unimi.it)
  • Expression profiles of clustered genes were further assessed at the mRNA and protein levels in subsets of circulating PBMo (GR1- vs GR1+) and lung resident macrophages (alveolar vs interstitial Mϕ). (biomedcentral.com)
  • The altered expression of a number of genes at the mRNA level is known to be essential for progression through the cell cycle, however, a comprehensive gene expression profile of human cells remains to be completed. (ox.ac.uk)
  • In conclusion, our FFPET-optimized workflow enables the detection of more genes than previous, nonoptimized approaches, opening new possibilities for the discovery, validation, and clinical application of mRNA biomarkers in human diseases. (biomedcentral.com)
  • A two-gene panel consisting of CDC20 and PTGDS had a better prognostic value compared with CDC20 or PTGDS alone in the TCGA cohort ( P =0.026 and 0.039). (portlandpress.com)
  • Gene expression array data were used as a training set to screen for single genes with prognostic impact. (scilifelab.se)
  • The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. (scilifelab.se)
  • Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. (scilifelab.se)
  • Whole genome microarray gene expression profiling is the 'gold standard' for the discovery of prognostic and predictive genetic markers for human cancers. (biomedcentral.com)
  • In order to assess the transcriptional profile of circulating and lung resident mononuclear phagocyte phenotypes, PBMo, lung Mϕ and lung DC from naïve mice were flow-sorted to high purity, and their gene expression was compared by DNA microarrays on a genome-wide scale. (biomedcentral.com)
  • Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. (scilifelab.se)
  • In contrast, interstitial and even more pronounced alveolar Mϕ, stepwise downregulate gene expression of these traffic relevant communication molecules, but strongly upregulate a distinct set of matrix metallopetidases potentially involved in tissue invasion and remodeling. (biomedcentral.com)
  • In clustering, the hypothesis that functionally related genes and/or phenotypically similar samples will display correlated gene expression patterns motivates the search for groups of genes or samples with similar expression patterns. (biomedcentral.com)
  • Differential regulation of selected genes was validated by quantitative PCR and on protein level by flow cytometry. (biomedcentral.com)
  • We empirically evaluate the SOLL model on a set of cell-cycle regulation data, demonstrating its effectiveness in discovering the temporal patterns of correlated genes and its usefulness as a tool for generating and visualizing interesting hypotheses. (elsevier.com)
  • Overlapping DEGs were then evaluated for gene ontology (GO), pathways enrichment, DNA methylation, protein-protein interaction (PPI) network analysis as well as survival analysis. (portlandpress.com)
  • Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup. (scilifelab.se)
  • The vast number of gene transcripts assayed by modern microarrays (10 5 -10 6 ) has driven forward our understanding of biological processes tremendously, elucidating the genes and regulatory mechanisms that drive specific phenotypes. (biomedcentral.com)
  • DNA microarrays are a high-throughput technology useful for functional genomics and gene expression analysis. (elsevier.com)
  • GeneChip containing microarrays of oligonucleotides corresponding to over 12 000 human genes were employed to profile differential gene expression in G1 and G2. (ox.ac.uk)
  • Quantitative determination of genome-wide expression levels via microarray technology also provides a powerful approach for comparative analysis of normal and neoplastic tissues. (biomedcentral.com)
  • This method may be used to classify samples based on multi-gene expression patterns and to identify pathways associated with phenotype, without relying upon the differential expression of individual genes. (biomedcentral.com)
  • By applying the PDM on a pathway-by-pathway basis and identifying those pathways that permit unsupervised clustering of samples that match known sample characteristics, we show how the PDM may be used to find sets of mechanistically-related genes that may play a role in disease. (biomedcentral.com)
  • Temporal expression profiling is important in many applications, including developmental studies, pathway analysis, and disease prognosis. (elsevier.com)
  • By contrast, after vaccination with the pneumococcal vaccination, there was enrichment of dendritic cells, monocytes and interferon related signatures in capillary blood, whilst at 24h there was enrichment for T and NK cell related signatures in venous blood.These data show differences between venous and capillary gene expression both at baseline, and post vaccination, which may impact on the conclusions regarding immunological mechanisms drawn from studies using these different sampling methodologies. (ox.ac.uk)
  • All cases were successfully profiled by GEP on formalin-fixed, paraffin-embedded tissue samples. (elsevier.com)
  • Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. (scilifelab.se)
  • Gene expression profiling is a technology for identifying the genes that are active in a given sample of cells or tissue. (biomedcentral.com)
  • So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap. (scilifelab.se)
  • One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics. (scilifelab.se)
  • Evaluation of TransPlex Whole Transcriptome Amplification method for microarray gene expression profiling / C. Peano, M. Severgnini, I. Cifola, E. Rizzi, G. De Bellis, C. Battaglia. (unimi.it)
  • In addition, in silico probe set redesign improved sequence detection sensitivity and, thus, may rescue potentially significant small-magnitude gene expression changes that could otherwise be diluted by the overall probe set background. (biomedcentral.com)
  • We describe an extension and application of a new unsupervised statistical learning technique, known as the Partition Decoupling Method (PDM), to gene expression microarray data. (biomedcentral.com)
  • While many microarray data are generated in sequence, most expression analysis tools are not utilizing the temporal information. (elsevier.com)
  • In this paper, we develop a learning method designed for temporal gene expression profiling from massive DNA-microarray data. (elsevier.com)
  • Overall, the present study identified a set of novel genes and pathways that may play a significant role in the initiation and progression of DLBCL. (portlandpress.com)
  • Diffuse large B-cell lymphoma (DLBCL) is the most common hematologic malignancy, however, specific tumor-associated genes and signaling pathways are yet to be deciphered. (portlandpress.com)
  • It attempts to learn probabilistic lattice maps of the gene expressions, which are then used for profiling the trajectories of temporal expressions of co-regulated genes. (elsevier.com)
  • Our data provide new insight in the changes of the genetic profiles of PBMo and their lung descendents, namely DC and Mϕ under non-inflammatory, steady-state conditions. (biomedcentral.com)
  • We describe the PDM in detail and apply it to three publicly available cancer gene expression data sets. (biomedcentral.com)
  • We show that the PDM is a useful tool for the analysis of gene expression data from complex diseases, where phenotypes are not linearly separable and multi-gene effects are likely to play a role. (biomedcentral.com)
  • After three independent experiments the resultant data was filtered and a set of genes was compiled based on at least threefold-altered expression, no background noise in determining expression and observation in all experiments. (ox.ac.uk)
  • The increased use of microarray expression profiling to study both the molecular biology of cancer and the cellular physiology of difficult-to-isolate cell types has led to a growing need for methods that allow the use of limiting quantities of RNA. (unimi.it)
  • It provides an affordable approach to examine differential gene-expression analysis between groups of samples, such as various treatments, time-points, or disease versus control samples. (genomescan.nl)
  • Here we sought to monitor the differential gene expression of genes after the transition of G2 cells into G1 prior to the restriction point. (ox.ac.uk)