• Knowledge of the expression patterns of HE4 in our survey is useful for application in histopathologic diagnosis, and should be taken into consideration in future studies that examine the role of HE4 as a serological tumor biomarker or as a target for gene-based therapy. (nature.com)
  • Such a segment in the tumor genome may harbor either oncogenes or tumor suppressor genes depending on whether they are present in increased or decreased copy number, respectively. (biomedcentral.com)
  • G-Protein Signaling Protein-17 (RGS17) Is Upregulated and Promotes Tumor Growth and Migration in Human Colorectal Carcinoma. (nih.gov)
  • Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD , indicating a potential tumor suppressor function for this gene. (biomedcentral.com)
  • PTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma. (biomedcentral.com)
  • We further demonstrate that PTPRD has a tumor suppressor function in neuroblastoma through dephosphorylating and destabilizing AURKA, leading to a downstream decrease of MYCN protein. (biomedcentral.com)
  • In order to further examine the possibility that PTPRD acts as a tumor suppressor gene in neuroblastoma, we initially analyzed the levels of PTPRD mRNA transcripts in a set of 88 neuroblastoma tumors using the R2: microarray analysis and visualization platform ( http://r2.amc.nl ) (University of Amsterdam). (biomedcentral.com)
  • Traditional methods of gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. (wikipedia.org)
  • Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. (biomedcentral.com)
  • Using an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. (biomedcentral.com)
  • Past genomic studies have comprehensively described the organization of the bacterial chromosome, for example in terms of gene localization, order and orientation. (biomedcentral.com)
  • Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. (biomedcentral.com)
  • Genomic DNA copy number variation is a hallmark of cancer and can lead to alteration in the expression and functions of genes residing within the affected chromosomal region [ 5 ]. (biomedcentral.com)
  • The resolution of array-CGH is determined by the genomic spacing of the array elements thus is much more improved compared to previous conventional CGH [ 10 - 12 ]. (biomedcentral.com)
  • We of Buruli ulcer, is hampered by the striking lack of genetic di- used this method for the differential genomic analysis of M. versity of this emerging pathogen. (cdc.gov)
  • CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. (frontiersin.org)
  • Standard chromosome analysis by G-banding has a limited resolution, but molecular cytogenetic techniques, such as multi-subtelomeric FISH, microdeletion FISH, multicolour FISH and comparative genomic hybridisation (CGH), have played an important role for the diagnosis of MR during the past decade. (bmj.com)
  • This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones. (nih.gov)
  • Screening for chromosomal imbalances by array CGH, whether using cDNA 23 or BAC clones, 24 has mainly been performed on cancer samples, 25- 30 which usually contain large gene dose alterations. (bmj.com)
  • All chromosome imbalances were size mapped using BAC and PAC clones based on clone mapping databases ( www.ensembl.org , July 2003), except for case 9, which was size mapped using a chromosome 22 specific micro-array. (bmj.com)
  • A tissue-specific cDNA microarray was generated using a set of sequence non-redundant EST clones collected from mouse retina. (biomedcentral.com)
  • Indeed, bacterial genomes carry, on average, from 78% (for genomes containing the polymerase PolC) to 58% (for the other genomes) of their genes on the leading strand [ 3 ]. (biomedcentral.com)
  • PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
  • strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
  • Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)
  • Genetic analyses suggest recent diver- adapted specialist. (cdc.gov)
  • For mycobacteria such as Myco- understood, partly because no molecular typing method bacterium tuberculosis and M. ulcerans , low intraspecies with suffi ciently high resolution for microepidemiologic diversity limits the use of genetic fi ngerprinting techniques analyses is available. (cdc.gov)
  • For M. tuberculosis , M. bovis , and the various cus sequence typing, restriction fragment length polymor- bacillus Calmette-Guérin daughter strains, genome-wide phism, and fi ngerprinting using variable number of tandem microarray analyses have identifi ed large sequence poly- repeats have shown an apparent lack of genetic diversity of morphisms ( 4 , 8 - 10 ). (cdc.gov)
  • Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
  • In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations. (clinicforspecialchildren.org)
  • Genetic analysis of biomass and photosynthetic parameters in wheat grown in different light intensities [J]. J Integr Plant Biol. (jipb.net)
  • Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
  • Genetic analysis includes procedures for genotyping, SNP (single nucleotide polymorphism) detection, strain identification and various other procedures. (ddw-online.com)
  • The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. (lookformedical.com)
  • Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
  • Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. (biomedcentral.com)
  • All 11 selected SNPs within candidate genes were verified by polymerase chain reaction (PCR) sequencing. (bmj.com)
  • Differential expression of six of seven candidate genes were confirmed. (bmj.com)
  • Instead of employing a whole-genome or exome strategy, they performed deep resequencing of carefully-chosen candidate genes in pools of ~20 samples. (massgenomics.org)
  • The gene encoding Sec31B is located on chromosome 10q24 and contains 29 exons. (biologists.com)
  • PCR analysis of exon utilization reveals massive alternative mRNA splicing of Sec31B, with just 16 exons being constitutively utilized in all transcripts. (biologists.com)
  • The 145 kb target space comprised 653 exons from nuclear genes (138 kb) and two mtDNA regions (7 kb). (massgenomics.org)
  • Sequences of DNA in the genes that are located between the EXONS. (lookformedical.com)
  • The presence of a stop codon in exon 13 generates two families of Sec31B gene products (each displaying additional patterns of mRNA splicing): a group of full-length proteins (hereafter referred to as Sec31B-F) and also a group of truncated proteins (hereafter referred to as Sec31B-T), distinguished by their utilization of exon 13. (biologists.com)
  • HE4 is one of more than 8900 different human genes represented on U95a GeneChips (Affymetrix, Santa Clara, CA, USA), which we used previously to develop a molecular classification of 175 human carcinomas based on patterns of gene expression. (nature.com)
  • In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. (nih.gov)
  • While expression patterns of many proteins in human medulloblastoma subgroups have been discerned, the expression pattern of GPCRs in medulloblastoma has not been investigated. (biomedcentral.com)
  • The results showed evolutionary patterns of single molecule mutational gene expression from benign hepatocytes to liver cancer cells. (elifesciences.org)
  • Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. (jipb.net)
  • On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. (jipb.net)
  • Six individual gene expression clusters were identified based on expression patterns of transcripts through retina development. (biomedcentral.com)
  • Sood R, Zehnder JL, Druzin ML, Brown PO "Gene expression patterns in human placenta. (openwetware.org)
  • Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). (nih.gov)
  • Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
  • We have also attempted to verify a series of differentially expressed candidate susceptibility genes to lung tumours in our previous microarray analysis with semiquantitative reverse transcriptase PCR (RT-PCR). (bmj.com)
  • We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
  • Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. (cancerindex.org)
  • Tiling arrays are a useful tool in genome-wide association studies. (wikipedia.org)
  • With the release of a genome wide SNPs database, it has become feasible to analyse these genetically determined QTLs for genes polymorphic in these strains. (bmj.com)
  • Recognition of a similarly affected second cousin prompted a genome-wide homozygosity mapping study using high-density single nucleotide polymorphism (SNP) arrays. (clinicforspecialchildren.org)
  • This study provides a complementary genome-wide view of common gene dynamics and a broad molecular classification of mouse retina development. (biomedcentral.com)
  • The genes encoding these proteins are highly conserved within the Trichinellids, are constituents of mL1 ESP and localized in the parasite stichosome. (westminster.ac.uk)
  • Therefore, identification and characterization of the chromosome regions with DNA copy number alteration in Western and Asian countries is important to unravel the mechanism underlying lung tumorigenesis. (biomedcentral.com)
  • Zhang B, Liu X, Zhao G, Mao X, Li A, Jing R (2014) Molecular characterization and expression analysis of Triticum aestivum squamosa‐promoter binding protein‐box genes involved in ear development. (jipb.net)
  • Buess M, Nuyten DS, Hastie T, Nielsen T, Pesich R, Brown PO "Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. (openwetware.org)
  • Background Clustering gene expression data has been an important problem in computational biology. (columbiagypsy.net)
  • Identification of regions with copy number aberrations and the genes involved thus offers a basis for better understanding of cancer development [ 6 ]. (biomedcentral.com)
  • 31, 32 In this report we used a cDNA micro-array and two BAC clone micro-arrays on 10 previously identified cases containing 16 cryptic chromosome aberrations, to test their performance for the detection of small imbalances. (bmj.com)
  • The 10 cases contained altogether 16 aberrations, with sizes ranging from 1.3 to 20.5 Mb, and they were located on 15 different chromosome arms. (bmj.com)
  • A subset of high quality and rare information, retrieved and organized by systematic literature- searching tools from existing databases, and related to a subset of genes functioning together in '-omic' sciences. (genomicglossaries.com)
  • However, biologically a gene or a sample could participate in multiple biological pathways, and a cellular process is generally active only under a subset of genes or experimental conditions. (columbiagypsy.net)
  • In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. (wikipedia.org)
  • Earlier studies on chromosome 21 and 22 showed the power of tiling arrays for identifying transcription units. (wikipedia.org)
  • Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. (biomedcentral.com)
  • The asymmetry of the distribution of the genes between the two strands of DNA is explained as being a means of minimizing interruptions in gene transcription due to collisions between the DNA and RNA polymerases. (biomedcentral.com)
  • Gene organization in the bacterial chromosome has very well known effects on transcription and a standard example is the organization of genes into operons, which allows for a sophisticated regulation of gene expression [ 9 ]. (biomedcentral.com)
  • 3 Given its homology and comparable transcription profile with known leukocyte protease inhibitors in the WFDC family of proteins, HE4 also presumably has a role in natural immunity. (nature.com)
  • PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)
  • This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. (cancerindex.org)
  • Applying the BBC algorithm to the yeast expression data, we noticed that most the biclusters we discovered are backed by significant biological evidences, such as for example enrichments of gene features and transcription aspect binding sites in the corresponding promoter sequences. (columbiagypsy.net)
  • The BBC model can simply handle lacking data via Monte Carlo imputation and gets the potential to end up being extended to integrated study of gene transcription networks. (columbiagypsy.net)
  • Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
  • Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe intensively for sequences which are known to exist in a contiguous region. (wikipedia.org)
  • Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. (nih.gov)
  • Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. (biomedcentral.com)
  • Soen Y, Mori A, Palmer TD, Brown PO "Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. (openwetware.org)
  • Another study with Arabidopsis used high-density oligonucleotide arrays that cover the entire genome. (wikipedia.org)
  • Here, we examined the expression of the HE4 gene and protein in a large series of normal and malignant adult tissues by oligonucleotide microarray and tissue microarray, respectively. (nature.com)
  • Here, we used oligonucleotide and tissue microarrays to survey HE4 gene and protein expression in a large group of malignant and normal tissues from adults. (nature.com)
  • The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. (nih.gov)
  • 4, 5 Four QTLs identified as pulmonary adenoma susceptibility (Pas) loci 1-4 have been mapped, respectively, to mouse chromosomes 6, 17, 19, and 9. (bmj.com)
  • And research published in January documented the first instance of the resulting gene-dosage effect on disease susceptibility: the effect of copy number. (the-scientist.com)
  • Targeting Dvl proteins increases imatinib susceptibility of the K562 and MEG-01 cell lines. (bvsalud.org)
  • Sequence of the cloned cDNAs revealed the single nucleotide mutation in two alternatively spliced isoforms of slow TnT mRNA. (clinicforspecialchildren.org)
  • Third, even using currently available comprehensive arrays, tissue-specific genes are still under-represented, including alternatively spliced variants or genes that are only briefly expressed in a tissue-specific pattern. (biomedcentral.com)
  • In today's research laboratory, two common ways that gene expression is assessed is by using quantitative polymerase chain reaction techniques (QTPCR) for monitoring expression of smaller numbers of genes, and by employing DNA microarrays for the highly parallel monitoring of thousands of genes (or the whole transcriptome). (ddw-online.com)
  • The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
  • 19- 22 Yet none of these techniques is able to offer a high resolution screening of the whole genome for chromosome imbalances. (bmj.com)
  • Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
  • Mutant TNNT1 cDNA is translationally active in Escherichia coli and non-muscle eukaryotic cells, producing the expected truncated slow TnT protein. (clinicforspecialchildren.org)
  • In the developing male (XY) gonad, sex-determining region of the Y (SRY) protein acts to up-regulate expression of the related gene, SOX9 , a transcriptional regulator that in turn initiates a downstream pathway of testis development, whilst also suppressing ovary development. (plos.org)
  • Halbleib JM, Sääf AM, Brown PO, Nelson WJ "Transcriptional Modulation of Genes Encoding Structural Characteristics of Differentiating Enterocytes During Development of a Polarized Epithelium In Vitro. (openwetware.org)
  • Sääf AM, Halbleib JM, Chen X, Tsan Yuen S, Yi Leung S, Nelson WJ, Brown PO "Parallels between Global Transcriptional Programs of Polarizing Caco-2 Intestinal Epithelial Cells In Vitro and Gene Expression Programs in Normal and Colon Cancer. (openwetware.org)
  • Klapholz-Brown Z, Walmsley GG, Nusse YM, Nusse R, Brown PO "Transcriptional program induced by wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments. (openwetware.org)
  • Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
  • Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • While protein expression is dictated by the level of gene expression, the structure and function of the protein is largely determined by the isoforms of the mRNA of a given gene and are impacted by mutations or other structural alterations to the amino acids ( Faustino and Cooper, 2003 ). (elifesciences.org)
  • Gene expression profiles obtained without artifacts introduced by isolation procedures or gene mutations provide a valuable overview of retina development under natural developmental conditions. (biomedcentral.com)
  • Key to the success of these studies is the accuracy of the allelic frequency calculations, the ability to identify false-positives arising from assay variability and the ability to better resolve association signals through analysis of neighbouring SNPs. (clinicforspecialchildren.org)
  • 80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. (mdpi.com)
  • It was Besides referred that the suitable types of pyrimidines of rodents at such and bulk Advances( PPT as the protein of chloride, rice, the receptor of copy after coding the vector) mRNA gene analysis combining the polymorphism authors at older promoters( 8, 10, 11). (scoutconnection.com)
  • FMI-1 has a unique and strikingly conserved structure with cadherin and C-terminal G-protein coupled receptor domains and could mediate cell-cell adhesion and signaling functions. (biologists.com)
  • Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. (biomedcentral.com)
  • Protein tyrosine phosphatase receptor delta ( PTPRD ) is an important regulator of axon growth and guidance and is highly expressed in the central nervous system where it functions as a transmembrane homophilic neuronal cell adhesion molecule [ 1 ]. (biomedcentral.com)
  • Specific probes are present in millions of copies (as opposed to only several in traditional arrays) within an array unit called a feature, with anywhere from 10,000 to more than 6,000,000 different features per array. (wikipedia.org)
  • Only about 10,000 of these genes have been annotated by the sea urchin sequencing team. (blogspot.com)
  • This organization of the chromosome can be described as being an adaptive and functional tool, essential for the survival of the bacterial cell. (biomedcentral.com)
  • It has also been shown that neighbouring genes in a bacterial chromosome tend to be co-expressed, even if they are not in the same operon [ 10 ], suggesting the existence of a "supra-operonic" organization [ 11 ]. (biomedcentral.com)
  • Using tissue microarrays and full tissue sections of normal and 448 neoplastic tissues, HE4 immunoreactivity was found in normal glandular epithelium of the female genital tract and breast, the epididymis and vas deferens, respiratory epithelium, distal renal tubules, colonic mucosa, and salivary glands, consistent with HE4 gene expression. (nature.com)
  • The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. (nih.gov)
  • Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. (nih.gov)
  • An integrated bioinformatics analysis based on the array data from the GEO database was conducted to view the differential expression of CMTM4 across multiple cancers and their corresponding control tissues. (biomedcentral.com)
  • Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
  • Then the chimeric RNA molecules are converted into cDNA libraries for high-throughput sequencing. (nih.gov)
  • As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis. (springer.com)
  • These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
  • We hypothesized that analysis of GPCR expression would identify clear subsets of medulloblastoma and suggest distinct GPCRs that might serve as molecular targets for both imaging and therapy. (biomedcentral.com)
  • As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. (biomedcentral.com)
  • The PRDM9 zinc finger array is highly polymorphic both within and between species (Berg et al. (springer.com)
  • Of these, 3,114 were single genes confined to a single species. (blogspot.com)
  • Protein mutation is essential in species evolution and cancer development. (elifesciences.org)
  • Expression analysis of mutant XY gonads at the same stage also reveals a dramatic reduction in Sox9 and, crucially, Sry at the transcript and protein levels. (plos.org)
  • The parts of a transcript of a split GENE remaining after the INTRONS are removed. (lookformedical.com)
  • When expressed as a fusion protein with eYFP in cultured cells, Sec31B-F associates with the endoplasmic reticulum and with vesicular-tubular clusters, displays restricted intracellular movement characteristic of COPII vesicle dynamics, co-distributes on organelles with Sec13, Sec31A and Sec23 (markers of the COPII coat), and concentrates with ts045-VSV-G-CFP (VSV-G) when examined early in the secretory pathway or after temperature or nocodazole inhibition. (biologists.com)
  • CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. (frontiersin.org)
  • Conclusions The BBC algorithm is certainly been shown to be a robust model-structured biclustering method that may discover biologically significant gene-condition clusters in microarray data. (columbiagypsy.net)
  • Second, all genes and conditions have to be assigned to clusters. (columbiagypsy.net)
  • A biclustering scheme that produces gene and condition/sample clusters simultaneously can model the situation where a gene or a condition is usually involved in several biological functions. (columbiagypsy.net)
  • 2] proposed a modified version of one-way clustering using a Bayesian model in which genes can belong to multiple clusters or none of the clusters. (columbiagypsy.net)
  • Different genes in the same functional clusters are expressed in the different developmental stages, suggesting that cells might change gene expression profiles from differentiation to maturation stages. (biomedcentral.com)
  • The identification of novel genes that are functionally involved in the initiation and progression of ccRCC may provide more sophisticated early diagnostic and further therapeutic strategies. (biomedcentral.com)
  • Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. (biomedcentral.com)
  • Human epididymis protein 4 (HE4) was first identified in the epithelium of the distal epididymis and originally predicted to be a protease inhibitor involved in sperm maturation. (nature.com)
  • We propose that large-scale changes in gene regulation during development are necessary for the final maturation and function of the retina. (biomedcentral.com)
  • Dishevelled (Dvl) is a scaffold protein that transmits Wnt signals to downstream effector molecules via both canonical and non-canonical Wnt signaling pathways. (bvsalud.org)
  • Chromatin immunoprecipitation allows binding sites of proteins to be identified. (wikipedia.org)
  • Proteins that bind to chromatin are cross-linked in vivo, usually via fixation with formaldehyde. (wikipedia.org)
  • The chromatin is then fragmented and exposed to antibodies specific to the protein of interest. (wikipedia.org)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • 2009 ). At a larger scale, DSB formation occurs in the context of a specific chromosome architecture that consists of chromatin loops anchored to a proteinaceous axis (Zickler and Kleckner 1999 ). (springer.com)
  • DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)
  • LncRNAs are involved in a wide range of regulatory mechanisms that impact gene expression, including chromatin remodeling, modulation of alternative splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation [ 5 ]. (biomedcentral.com)
  • 1) How many of these predicted kinases are real genes? (ddw-online.com)
  • 2010 ). PRDM9 includes several functional domains, such as a DNA-binding zinc finger array, a histone lysine methyltransferase PR/SET (PRDI-BF1 and RIZ1 homology) domain, and a Krüppel-associated box (KRAB)-related domain. (springer.com)
  • This study provides a significant beginning of functional analysis of SBP-box genes in wheat. (jipb.net)
  • Functional analyses of an E3 ligase gene AIP2 from wheat in Arabidopsis revealed its roles in seed germination and pre-harvest sprouting [J]. J Integr Plant Biol. (jipb.net)
  • Within the same functional classes, however, different gene populations were expressed in distinct developmental phases. (biomedcentral.com)
  • A growing body of evidence shows that lncRNAs play important functional roles in diverse biological processes, such as epigenetic regulation, cell cycle regulation, cellular growth and differentiation, by regulating the level of target genes [ 3 , 4 ]. (biomedcentral.com)
  • CMTM4 is a member of this family and is located at chromosome 16q22.1, a locus that harbours a number of tumour suppressor genes. (biomedcentral.com)
  • With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and understand, it no longer suffices to rely on studies of one gene, gene product, or process at a time. (genomicglossaries.com)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • This is a perfect illustration of the mutual influence between gene expression levels and chromosomal organization in bacteria. (biomedcentral.com)
  • We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. (biomedcentral.com)
  • Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH. (wikipedia.org)
  • PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher order architectures, and RNA:RNA interactions in trans across the transcriptome. (nih.gov)
  • Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. (elifesciences.org)
  • In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome. (elifesciences.org)
  • The HE4 (WFDC2) gene encodes a WAP-type four disulphide core domain-containing protein with a presumptive role in natural immunity. (nature.com)
  • This gene encodes a member of the regulator of G-protein signaling family. (nih.gov)
  • The method of sequencing cDNA to find transcribed genes also runs into problems, such as failing to detect rare or very short RNA molecules, and so do not detect genes that are active only in response to signals or specific to a time frame. (wikipedia.org)
  • Recent advances in biological technologies, such as tiling arrays and RNA deep sequencing (RNA-seq), have made it possible to survey the transcriptomes of many organisms to an unprecedented degree [ 6 ]. (biomedcentral.com)
  • High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)
  • Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
  • In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
  • A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). (nih.gov)
  • Despite the large chromosome fragments involved in the unbalanced translocation in this case, repeated standard G-band analysis could not reveal this rearrangement due to the similarity in the banding pattern of the chromosome fragments involved. (bmj.com)
  • 3 Identification of the genes predisposing to cancer could yield targets for treatment or chemoprevention. (bmj.com)
  • Identification of the genes predisposing to mouse lung cancer could have considerable implications for diagnosis, treatment, or chemoprevention of lung cancer in humans. (bmj.com)
  • DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
  • The mutation in brush causes a small change in a protein belonging to the CNGC family. (elifesciences.org)
  • The byg mutation is an A to T transversion causing a premature stop codon in the gene encoding MAP3K4 (also known as MEKK4), a mitogen-activated protein kinase kinase kinase. (plos.org)
  • Our data indicate, for the first time, a requirement for MAPK signaling in the developing XY gonad in order to facilitate normal expression of SRY and the downstream testis-determining genes and also suggest that reduced dosage of MAP3K4 may be the cause of a previously described autosomal sex-reversing mutation in the mouse. (plos.org)
  • A nonsense mutation at codon Glu180 in exon 11 of slow skeletal muscle troponin T (TnT) gene (TNNT1) causes an autosomal-recessive inherited nemaline myopathy. (clinicforspecialchildren.org)
  • Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. (elifesciences.org)
  • The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. (elifesciences.org)
  • Among 4,180 transcripts that changed significantly during development, approximately 2/3 of the genes were expressed at high levels up until PN5 and then declined whereas the other 1/3 of the genes increased expression from PN5 and remained at the higher levels until at least PN21. (biomedcentral.com)
  • A gene expression profile analysis has been performed and the results indicated that CBPDA is significantly increased the expression of five genes: CARD9, BNIP, TNFRSF-1B, TNFRSF25 and TNF-alpha, that have an important role in induction of apoptosis. (longdom.org)
  • We showed SMAD1, AHR, mTOR, BRD7 protein expressions are significantly affected by Dvl silencing and overexpression in CML cell lines. (bvsalud.org)
  • Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked. (nih.gov)
  • of a 174-kb plasmid that bears a cluster of genes necessary for the synthesis of the polyketide toxin mycolactone. (cdc.gov)
  • Our study provides an invaluable database revealing common and differential imbalance regions at specific chromosomes among Asian and Caucasian lung cancer patients. (biomedcentral.com)
  • In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)
  • Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. (nih.gov)
  • Transfective expression in undifferentiated myoblasts produced slow TnT mRNA but not a detectable amount of truncated or intact slow TnT proteins, indicating a muscle cell-specific proteolysis of TnT when it is not integrated into myofilaments. (clinicforspecialchildren.org)
  • Site-specific iterations of biological clues or cumulative issues Compared at other models in the F2 Mechanisms of Inorganic and Organometallic thrive for using the solution of the processes of these cells and network or cycle proteins and Modelling interactions about sufficient capsids and genes of PPT sites. (scoutconnection.com)
  • Chromosome specific micro-arrays have however been used in a few cases to determine the critical regions in microdeletion disorders. (bmj.com)
  • This method was used to measure the number of copies of repeated genes such as rRNA genes (2) and to measure whether specific genes were under-replicated during the replication process used in forming polytene chromosomes (3). (ddw-online.com)
  • Palmer C, Diehn M, Alizadeh AA, Brown PO "Cell-type specific gene expression profiles of leukocytes in human peripheral blood. (openwetware.org)
  • Three specific modifications, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and N1-methylguanosine (m1G), are abundant in eukaryotic tRNAs and are particularly problematic for reverse transcriptases (RTs) by causing cDNA synthesis to stop or misincorporate. (cdc.gov)
  • 4, 5 The process involves use of many evenly spaced polymorphic DNA markers to create landmarks across each chromosome. (bmj.com)
  • At least three papers last summer dealt with the advantage of new technologies used to discover the extent to which these polymorphic rearrangements are duplications of genes found elsewhere in the genome. (the-scientist.com)
  • Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. (biomedcentral.com)
  • Revealing the intrinsic program of gene regulation that accompanies mammalian retinal development is a key step for eventual cure of many human retina diseases and blindness. (biomedcentral.com)
  • Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
  • Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. (nih.gov)
  • LOCUS BC070161 1482 bp mRNA linear HUM 11-APR-2007 DEFINITION Homo sapiens structural maintenance of chromosomes 4, mRNA (cDNA clone IMAGE:4252738), partial cds. (nig.ac.jp)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)