• The majority of the top 15 differentially expressed genes for each tissue were known to either be expressed in a tissue-specific manner or relate to specific functions of that tissue. (cambridge.org)
  • Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. (cambridge.org)
  • Additionally, in one of the experiments comparing liver and muscle expression, "two times the number of differentially expressed exons was discovered using the array," Xu told BioArray News this week. (genomeweb.com)
  • The differentially expressed genes can be classified as genes involved in protein synthesis, cell cycle, signal transduction, apoptosis, mitochondrial-related proteins, and immune responses. (usda.gov)
  • By integrating two datasets (GSE77459 and GSE92681) in the GEO database using the sva and limma packages of R, differentially expressed genes (DEGs) of pulpitis were identified. (researchsquare.com)
  • Differentially expressed miRNAs were identified using Affymetrix TAC software. (karger.com)
  • In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. (hindawi.com)
  • The R package was used for data mining and screening differentially expressed genes (DEGs). (hindawi.com)
  • In this study, a data mining strategy was used to obtain 2 microarray datasets of gastric cancer from the GEO database to identify differentially expressed genes (DEGs) associated with gastric cancer occurrence and progression. (hindawi.com)
  • Twelve genes were significantly differentially expressed when analyzed by at least two independent methods, and an additional five genes showed a strong a tendency toward differential expression. (biomedcentral.com)
  • Finally, the differentially expressed mRNA was confirmed with protein expression for some of the genes. (biomedcentral.com)
  • In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
  • Use of the Affymetrix Human GeneChip array and genomic. (cambridge.org)
  • Affymetrix GeneChip microarrays are a powerful tool to study global gene expression profiles and have been used on many species. (cambridge.org)
  • However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. (cambridge.org)
  • In this study, we demonstrate that gDNA-based probe selection on the Affymetrix Human U133+2 GeneChip array can be used to study gene expression profiles in sheep tissues. (cambridge.org)
  • Image: Courtesy of Rosetta Biosoftware The Rosetta Resolver system's Image Viewer application showing an Affymetrix GeneChip probe array. (the-scientist.com)
  • This week, Last maintained that Affy is committed to offering the "best, cutting-edge gene-expression tools available," and said that the GeneChip Human Transcriptome and Splice Junction array "is the next generation of these tools, offering an even better view of the transcriptome. (genomeweb.com)
  • Gene expression profiles were obtained using the Affymetrix human genome U95A GeneChip. (nih.gov)
  • Reverse-transcription polymerase chain reaction (RT-PCR) was performed to confirm the differential expression of genes obtained from Genechip analysis. (nih.gov)
  • In this study, we conducted a comprehensive chicken gene expression profiling using oligonucleotide-based Affymetrix GeneChip Chicken Genome Arrays. (usda.gov)
  • The data was analyzed with the Affymetrix GeneChip Command Console. (nih.gov)
  • Data reduction is an issue because Affymetrix GeneChip oligonucleotide microarrays assay each target mRNA with a set of 11 to 16 pairs of 25-nucleotide DNA probes. (biomedcentral.com)
  • Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. (bioconductor.org)
  • Besides demonstrating that the probe selection method can be used to study the ovine transcriptome, the benefits of this approach are that it can greatly increase the number of annotated and novel genes that can be studied beyond those currently possible using ovine- or bovine-specific microarrays. (cambridge.org)
  • 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)
  • 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)
  • 18 With the exception of the ovarian neoplasms, the same carcinomas analyzed for gene expression were also examined for HE4 by immunohistochemistry on tissue microarrays (see below). (nature.com)
  • According to lead author Weihong Xu, "lower technical variance with the microarrays translated to increased power for detecting low-level expression changes" compared to RNA-seq. (genomeweb.com)
  • Our technology follows the use of NGS or Sanger sequencing in discovery to take the workflow downstream with the validation performance of catalog or custom expression microarrays," he said. (genomeweb.com)
  • There have been dimensional increases in 'omics datasets, including introduction of new types of data, increases in the size of individual datasets, increases in the varieties of experimental platforms within a given data type (e.g. more varieties of gene expression microarrays), and very large increases in the total number of datasets being generated. (biomedcentral.com)
  • The ankylosed calluses were harvested at days 14 and 28 postoperatively and analyzed by Affymetrix OviGene-1_0-ST microarrays. (medscimonit.com)
  • Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. (medscape.com)
  • Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. (medscape.com)
  • DNA microarrays are simply platforms that consist of small solid supports onto which the sequences from thousands of different genes are attached at fixed locations. (medscape.com)
  • Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. (medscape.com)
  • Conclusions: Microarrays are a powerful tool to identify biomarkers for obesity by analyzing differential gene expression profiles. (sages.org)
  • Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). (researchsquare.com)
  • A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)
  • DAVID was used to perform the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis for the different expression genes (DEGs). (medscimonit.com)
  • Ten DEGs, including 7 hub genes from PPI analysis, were confirmed by real-time PCR. (medscimonit.com)
  • Using the GSE19826 and GSE54129 datasets, a total of 550 DEGs were identified, including 248 upregulated and 302 downregulated genes. (hindawi.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)
  • GeneChips were washed and stained in the Affymetrix Fluidics Station 450. (nih.gov)
  • pooled RNA was applied to Human Genome U133 Plus 2.0 Affymetrix GeneChips. (bmj.com)
  • For each disease, the differential gene expression between inflamed- and non-inflamed colon tissue was analyzed. (bioconductor.org)
  • We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis. (bioconductor.org)
  • This study provides a differential gene expression profile between TMJ fibrous and bony ankylosis. (medscimonit.com)
  • The differential gene expression data analysis was per-formed using Affymetrix microarray suite 5.0 software. (cdc.gov)
  • Arthritis susceptibility genes were sought by analysis of differential gene expression between pristane-induced arthritis (PIA)-susceptible DA rats and PIA-resistant E3 rats. (biomedcentral.com)
  • Inguinal lymph nodes of naïve animals and animals 8 days after pristane injection were analyzed for differential gene expression. (biomedcentral.com)
  • Direct comparison of RA patients with control groups is difficult because any differential gene expression in RA may be masked by genetic and/or environmental differences between individuals. (biomedcentral.com)
  • However, animal models of RA are well suited for analysis of differential gene expression because it is possible to analyze many individuals in which genetic background, environmental exposure and disease stage can be controlled. (biomedcentral.com)
  • In the present study, inguinal lymph nodes from the PIA-susceptible DA rat and from the PIA-resistant E3 strain were analyzed for differential gene expression using Affymetrix technology (Affymetrix, Inc., Santa Clara, CA, USA). (biomedcentral.com)
  • This study uses microarray technology to evaluate differential gene expression profiles in obese patients undergoing bariatric surgery versus non-obese controls. (sages.org)
  • PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. (nature.com)
  • Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable. (nature.com)
  • However, little information has been gathered to date regarding the genomic location of drought-regulated genes, either expressed throughout plant development or at late reproductive stages influencing seed yield and quality. (biomedcentral.com)
  • All genes have functions that are potentially important for arthritis, and nine of the genes are located within genomic regions previously associated with autoimmune disease. (biomedcentral.com)
  • To identify potential mechanisms underlying expression changes, genomic DNA was bisulfite treated for pyrosequencing of key CpG island 'shores' and promoter regions, and chromatin was prepared from both hippocampal tissue and a hippocampal-derived cell line to assess modifications of histones. (nih.gov)
  • The gastric cancer microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. (hindawi.com)
  • We extracted gene expression profiles from mouse macrophages from the GEO dataset, GSE152795 using the GEO2R webtool. (degruyter.com)
  • Celsius, the largest co-normalized microarray dataset of Affymetrix based gene expression, was used to calculate the correlation between all possible gene pairs on all platforms, and generate stored indexes in a web searchable format. (discovermagazine.com)
  • Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). (hindawi.com)
  • This workflow is directly applicable to current "Gene" type arrays, e.g. the HuGene or MoGene arrays, but can easily be adapted to similar platforms. (bioconductor.org)
  • These arrays contain probes for 32,773 chicken transcripts corresponding to more than 28,000 chicken genes. (usda.gov)
  • These chicken genome arrays have considerable promise as a valuable tool in understanding the molecular mechanism regulating MDV cytolytic and latent infection, and providing insights into the chicken gene expression pattern and associated biological pathways in response to different phases of viral pathogenesis. (usda.gov)
  • In the Advanced Online Publication of Nature Genetics , Tobey MacDonald and colleagues from the Children's National Medical Center , Washington, DC, report the use of oligonucleotide expression profiling (Affymetrix G110 cancer arrays) to define a set of genes that are prognostic for medulloblastoma metastasis (DOI:10.1038/ng731). (the-scientist.com)
  • In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. (bioconductor.org)
  • In conclusion, the results show that animal models are well suited for reproducible microarray analysis of candidate genes for arthritis. (biomedcentral.com)
  • Different statistical methods with varying selection criteria resulted in identification of similar candidate genes. (cdc.gov)
  • Array data are intended to provide candidate genes for hypothesis generation and further experimentation. (cdc.gov)
  • Array studies provide candidate genes to identify common mechanistic pathways in the effector phase, as well as mechanistic pathways unique to individual allergens. (cdc.gov)
  • By integrating different datasets from the Gene Expression Omnibus (GEO) database, we analysed a merged expression matrix of pulpitis, aiming to identify biological pathways and diagnostic biomarkers of pulpitis. (researchsquare.com)
  • Some genes, such as RELA and GADD45B , were predicted to extensively involve these critical pathways, indicating their potential functions in OA mechanisms. (frontiersin.org)
  • In conclusion, this study identified the significant modules, signaling pathways, and hub genes relevant to OA and highlighted the potential clinical value of anisomycin and MG-262 as novel therapies in OA management. (frontiersin.org)
  • In AAV groups, from the combined limma with GSEA using ClusterProfiler, we found both shared and unique gene sets and pathways for mice with wtHTT overexpression compared to mice with mHTT overexpression. (lu.se)
  • Multiple biosynthetic pathways such as sterol synthesis were among the top shared processes, where both unique and shared genes constituted leading-edge subsets. (lu.se)
  • Two of these genes, arginase 1 and eotaxin 1 are the focus of continuing investigations in mouse models of asthma regarding differences in mechanistic pathways depending on the allergen. (cdc.gov)
  • This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)
  • Two basic types of probe sets are created: 1) those that represent gene sequences uniquely, 2) those that represent multiple closely related gene sequences. (xenbase.org)
  • He then talks about a technology that was invented for a different purpose but was eventually applied to the specific problem of broadly monitoring the expression of gene sequences giving birth to Affymetrix. (stanford.edu)
  • However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)
  • In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), provid- ing a new powerful means for the classification, prediction of survival, and response to treatment of lym- phomas. (lu.se)
  • Background Gene expression profiling has successfully identified the prognostic significance of the host response in lymphomas. (haematologica.org)
  • These techniques can be used to analyze a large number of genes simultaneously and, when used for analysis in suitable experimental circumstances, provide valuable information on arthritis pathogenesis. (biomedcentral.com)
  • Functional analyses indicated that some of the genes induced by dragonfly larvae caused an increase in laminins necessary for cell adhesion in the extracellular matrix. (biomedcentral.com)
  • GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware, and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. (nih.gov)
  • Our unique blood analyses confirm previous tissue data from our lab and shed new light on the ensuing cascade of gene dysfunction associated with obesity. (sages.org)
  • mRNA expression data of energy-related genes were extracted from our whole retinal Affymetrix microarray data. (molvis.org)
  • mRNA expression was investigated by microarray and real-time PCR, and protein expression was analyzed by flow cytometry or ELISA. (biomedcentral.com)
  • In vitro transwell migration and quantitative reverse transcription polymerase chain reaction assays were used to assess myeloid cell chemotaxis and mRNA expression, respectively. (bvsalud.org)
  • Sunitinib therapy substantially mitigated both AAA formation and further progression of established AAAs, attenuated aneurysmal aortic MMP2 (matrix metalloproteinase) and MMP9 protein expression, inhibited inflammatory monocyte and neutrophil chemotaxis to VEGF-A, and reduced MMP2, MMP9, and VEGF-A mRNA expression in macrophages and smooth muscle cells in vitro. (bvsalud.org)
  • Design and Methods We collected 33 cases of T-cell/histiocyte-rich large B-cell lymphoma and 56 cases of nodular lymphocyte-predominant Hodgkin's lymphoma and performed microarray gene expression profiling on ten cases of each lymphoma, to obtain a better understanding of the lymphoma host response. (haematologica.org)
  • 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)
  • Bong I, Ng CC, Baharuddin P, Zakaria Z: MicroRNA expression patterns and target prediction in multiple myeloma development and malignancy. (karger.com)
  • The Affymetrix data revealed varied gene expression patterns of the ATP synthesizing and regulating enzymes found in the muscle, liver, and brain. (molvis.org)
  • Altered gene expression patterns were observed in 187 RNA transcripts with a signal log ratio of at least 0.8 (1.7 fold change). (cdc.gov)
  • The expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. (biomedcentral.com)
  • To analyze microarray datasets (34760 variables) and obtain functional implications of differential expression patterns, we used Linear Models for Microarray Data (limma) followed by Gene Set Enrichment Analysis (GSEA) using ClusterProfiler. (lu.se)
  • Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. (nature.com)
  • Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were QC'd using Expression Console software with Affymetrix default RMA Gene analysis settings. (nih.gov)
  • We report haplotyping data for 17 starch biosynthesis/degradation genes demonstrating the broad diversity among H. spontaneum accessions and H. vulgare landraces but rather limited genetic variance in the current elite breeding germplasm by fixing certain haplotypes. (biomedcentral.com)
  • The rapid development of gene chip high-throughput sequencing technology has accumulated much disease-related data since the past ten years. (hindawi.com)
  • Bioinformatics data mining of gene expression profiles using the Gene Expression Omnibus (GEO) database has led to identifying promising biomarkers associated with disease development [ 12 ]. (hindawi.com)
  • Data from these define genetic and non-genetic variation, define a measure of heritability for expression of individual genes, and provide the basis for a new method of data reduction for genetical genomics. (biomedcentral.com)
  • The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
  • Micro- array data from the ovalbumin and TMA model of asthma were also compared to previous data using Aspergillus as allergen to identify putative asthma `signature genes', i.e. genes up-regulated with all 3 allergens. (cdc.gov)
  • The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
  • Finally, we observed a significantly higher gene correlation shared between genes in disease networks associated with similar complex or Mendelian disorders. (discovermagazine.com)
  • We used the Partek workflow as well as Aroma to analyze the Affymetrix Mouse Exon 1.0ST array to generate the DE gene list. (nih.gov)
  • The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)
  • A point of note is that probe selection for the Affymetrix gene expression assay is biased towards the 3' end of transcripts. (xenbase.org)
  • For the eukaryotic gene expression assay, labeled antisense cRNA target is hybridized to the complementary 25mer probes. (xenbase.org)
  • 4. How do I get information about the Affymetrix assay? (xenbase.org)
  • A thorough description and diagram of the assay can be found on Affymetrix.com. (xenbase.org)
  • With this expanded license, Affymetrix intends to develop and market a platform with an assay menu of chromogenic-based applications of the bDNA technology. (aacc.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)
  • This study aims to explore its mechanism by defining changes in gene expression between neoplastic and normal tissue samples before and after treatment. (karger.com)
  • NGS is forcing customers to think about increasingly inclusive sets of transcripts, in particular alternative-splicing events as opposed to genes," said Last. (genomeweb.com)
  • The expression analysis of limited viral and host transcripts have revealed differences in gene expression pattern during cytolytic and latent phases of MDV infection. (usda.gov)
  • The technology allows evaluation of many gene transcripts at one time. (medscape.com)
  • [ 6 ] Both technologies use hybridization of labeled nucleic acid transcripts to measure the gene expression. (medscape.com)
  • Gene transcripts are represented by probe sets that consist of multiple 25mer oligonucleotides. (xenbase.org)
  • We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)
  • These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. (biomedcentral.com)
  • Identified genes, miRNAs, and TFs can be possible drug targets that may be used for the therapeutics. (degruyter.com)
  • A new, high-density array could help Affymetrix regain momentum in the gene-expression market. (genomeweb.com)
  • We compared the miRNA expression profiles of MM with 1q21 gains and MM with normal fluorescence in situ hybridisation (FISH) by gene expression array. (karger.com)
  • Affymetrix micro-array technology was used to identify gene expression alterations that had occurred during the adaptation. (lu.se)
  • The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. (medscape.com)
  • A Xenopus Consortium worked with Affymetrix to create the array. (xenbase.org)
  • 100ng of the total RNA was amplified and labeled using the Ovation RNA Amplification System V2 with the Ovation Whole Blood Reagent (NuGen) before hybridizing to an Affymetrix Focus Array containing over 8500 verified genes. (sages.org)
  • Examples of high molecular environmental factors are known to influence the development weight occupational allergens include proteases used in the and expression of asthma, and a vast array of triggers of asthma detergent industry, laboratory animal allergens, and ovalbumin have been identified. (cdc.gov)
  • Imports batches of Affymetrix array design. (lu.se)
  • Among these were, for example, several genes within the Wnt signalling pathway. (lu.se)
  • The expression of transthyretin, a protein shown to sequester Aβ and prevent amyloid fibril formation in vitro , and several genes in the insulin-signaling pathway, e.g., insulin-like growth factor-2, were increased selectively in the hippocampus of APP Sw mice. (jneurosci.org)
  • however, the expression in normal and malignant adult tissues has not been examined in detail. (nature.com)
  • Expression of selected retinal marker genes was studied via real-time PCR. (molvis.org)
  • Our goals were twofold: 1) to characterize the gene expression, protein expression, and activity of key synthesizing and regulating enzymes of energy metabolism in the whole mouse retina, retinal compartments, and/or cells and 2) to provide an integrative analysis of the results related to function. (molvis.org)
  • The combined results indicate that glycolysis is regulated by the compartmental expression of hexokinase 2, pyruvate kinase M1, and pyruvate kinase M2 in photoreceptors, whereas the inner retinal neurons exhibit a lower capacity for glycolysis and aerobic glycolysis. (molvis.org)
  • Expression of nucleoside diphosphate kinase, mitochondria-associated adenylate kinase, and several mitochondria-associated creatine kinase isozymes was highest in the outer retina, whereas expression of cytosolic adenylate kinase and brain creatine kinase was higher in the cones, horizontal cells, and amacrine cells indicating the diversity of ATP-buffering strategies among retinal neurons. (molvis.org)
  • These methods] have the potential of becoming powerful new tools to translate biomarker signatures to diagnostics that enable clinicians to personalize patient care," said George Bers, vice president and general manager of the gene expression business unit at Affymetrix. (aacc.org)
  • 687 genes differentiated tumor samples before and after treatment, among which 310 genes did not show the same differential expression in the placebo group or normal samples. (karger.com)
  • The differences in gene expression profiles induced by the two predators suggest that there are functional differences between the altered tail tissues of the two groups of tadpoles. (biomedcentral.com)
  • Many recent studies have reported the relationship between micro (mi)RNA expression and MM prognosis. (karger.com)
  • Then, the relationship between the expression level of the core genes and the prognosis of gastric cancer patients was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) database. (hindawi.com)
  • Gene expression profiling of lymphomas clearly illustrated that apart from the characteristics of the tumor cells, the microenvironment of the tumor also defines the profile of the lymphoma, and, more importantly, plays a role in predicting the prognosis. (haematologica.org)
  • Bioinformatic and pathway analysis was performed using Ingenuity pathway analysis (IPA), with gene validation by real time PCR. (bmj.com)
  • While transcription of prokaryotic protein-coding genes creates messenger RNA (mRNA) that is ready for translation into protein, transcription of eukaryotic genes leaves a primary transcript of RNA (pre-RNA), which first has to undergo a series of modifications to become a mature RNA. (wikipedia.org)
  • Results: We identified 97 upregulated genes and 125 downregulated genes with >1.5 fold change in obese patients versus controls. (sages.org)
  • Expression levels were normalized to GAPDH and fold- change of expression level was calculated using the comparative Ct method (2-Ct), as described previously ( 3 ). (cdc.gov)
  • Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. (hindawi.com)
  • The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)
  • EST stacks within the assembly, polyA sites and signals, biological evidence for expression, sequence annotation, and sequence orientation. (xenbase.org)
  • Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)
  • To explore the effect of millimeter wave exposure at low power density on gene expression in human keratinocytes (HaCaT). (nih.gov)
  • PAR-2 and ERGIC-53 genes in HaCaT cells were up-regulated by 3.5 mW/cm2 millimeter wave exposure for 4 times. (nih.gov)
  • ERGIC-53 gene was also up-regulated by 1.0 mW/cm2 millimeter wave exposure for 4 times. (nih.gov)
  • However, no significant change for PAR-2 expression was found after the same exposure. (nih.gov)
  • Millimeter wave exposure could affect gene expression in human keratinocytes, which might be related to the intensity and the times of exposure. (nih.gov)
  • We investigated the mechanisms by which radiofrequency (RF) fields exert their activity, and the changes in both cell proliferation and the gene expression profile in the human cell lines, A172 (glioblastoma), H4 (neuroglioma), and IMR-90 (fibroblasts from normal fetal lung) following exposure to 2.1425 GHz continuous wave (CW) and Wideband Code Division Multiple Access (W-CDMA) RF fields at three field levels. (powerwatch.org.uk)
  • The results confirm that low-level exposure to 2.1425 GHz CW and W-CDMA RF fields for up to 96 h did not act as an acute cytotoxicant in either cell proliferation or the gene expression profile. (powerwatch.org.uk)
  • This team from Japan has used both CW and simulated phone exposure at levels that would be typical of a phone user, to test whether or not they affect either cell proliferation or gene expression (both effects found in other research) in human cell lines (cancerous and healthy). (powerwatch.org.uk)
  • A further 80 genes showed greater than 5 fold differences in expression after exposure to dragonfly larvae and 81 genes showed altered expression after exposure to larval salamanders. (biomedcentral.com)
  • The higher expression of gremlin 1 and HIF1a genes after exposure to dragonfly larvae indicated an in vivo hypoxic reaction, while down-regulation of syndecan-2 may indicate impairment of angiogenesis. (biomedcentral.com)
  • Interestingly, a cluster of dysregulated genes regarding cell metabolism and lipid formation were identified. (sages.org)
  • Affymetrix probe sets typically consist of 11 to 16 probe pairs. (xenbase.org)
  • A biotin labeled cRNA transcript was synthesized, fragmented and hybridized to Affymetrix U133A oligonucleotide microarray. (cdc.gov)
  • In this article, we walk through an end-to-end Affymetrix microarray differential expression workflow using Bioconductor packages. (bioconductor.org)
  • Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype. (wikipedia.org)
  • These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. (wikipedia.org)
  • Protein-protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape. (researchsquare.com)
  • Gene expression profiles in the hippocampus and cerebellum of 6-month-old APP Sw mice were compared with age-matched controls. (jneurosci.org)
  • Thus the present study was designed to determine gene expression profiles in the hippocampus and cerebellum of 6-month-old APP Sw mice compared with age-matched controls and to identify potential mechanisms responsible for protecting neurons from Aβ toxicity. (jneurosci.org)
  • Existing methods that estimate tumor purity from a tumor gene expression profile adopt different analytical strategies (Supplementary Note 1 , 2 ). (nature.com)
  • We have tested heritability-weighted averages to define expression of a transcript and found that these allow detection of more QTLs than previously described methods. (biomedcentral.com)
  • Several alternative methods have been proposed to combine multiple probe-specific values into a single expression estimate. (biomedcentral.com)
  • Materials and Methods: We have adapted the Burkitt's lymphoma line Ramos to a serum-free medium that supports long-term survival and studied gene expression changes that occurred during the adaptation process. (lu.se)
  • Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions. (bioconductor.org)
  • The terms of the new deal allow Affymetrix to commercialize in situ Quanti-Gene ViewRNA products, in addition to giving the company exclusive rights to the use of alkaline phosphatase-conjugated oligonucleotides in bDNA methods. (aacc.org)
  • They analysed 23 primary medulloblastomas that were either metastatic (M+) or non-metastatic (M0) and identified 85 genes that served for class prediction (59 genes were upregulated in metastatic tumours and 26 were decreased). (the-scientist.com)
  • Using Merck's portfolio, HTG intends to develop new breast cancer diagnostics that will use gene expression testing to improve on risk of cancer recurrence prediction. (aacc.org)
  • The linkage/expression map is an informative resource in the context of characterizing the response of barley to drought stress. (biomedcentral.com)
  • therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. (frontiersin.org)
  • However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. (frontiersin.org)
  • Results Affymetrix analysis identified widespread changes in decidual gene expression following labour. (bmj.com)