reconstructing gene networks using gene expression profiles

... in gene- expression databases is growing rapidly To date, there are more than 60,000 experimental datasets stored in different geneexpression repositories; cf fig 1.1 Figure 1.1: Number of gene- expression ... cascade of genes affecting each other (b) Some “hub” genes may contain many edges to other non-relevant genes; hence these subnetworks may be missed because the genes with no differential expression ... 2.2 Background on class comparison using genes, pathways and subnetworks 2.2.1 Identifying differential gene expression 2.2.1.1 Fold-change ...

Ngày tải lên: 09/09/2015, 10:15

... study analyzed gene expression profiles in rat joints with SCW-induced arthritis using RAE230A GeneChip® oligonucleotide microarray (Affymetrix Inc.) We chose to profile gene expression in whole ... analyzed for differential gene expression using the RAE230A Affymetrix GeneChip® microarray (Affymetrix Inc., Santa Clara, CA, USA) In order to identify different patterns of gene expression during the ... differential gene expression of a particular gene of interest Previous studies have already shown that cell-specific gene expression patterns can indicate the presence of immune cells [20] RAE230A GeneChip®...

Ngày tải lên: 09/08/2014, 06:22

... also present (score 1) Gene- expression profiles and clustering As shown in Fig 3, 18 samples from 16 cases were clustered into two major groups based on their gene- expression profiles The dendrogram ... specific gene- expression profile that should explain the molecular nature of their etiological differences Candidate gene profiles in each group Using the SAM software, we examined 1,035 genes to ... several reports about gene- expression profiles in rheumatoid synovitis The analysis by Zanders and colleagues [16] showed an overall increased expression of inflammationrelated genes in synovial...

Ngày tải lên: 09/08/2014, 06:23

... SpA gene expression signature and the presence of novel biomarkers of disease Gene expression microarray Unfractionated whole blood collection and RNA isolation were performed using the PAXgene ... Study of gene expression using microarrays offers a novel approach to determining pathogenesis of diseases Analysis of peripheral blood in patients with systemic lupus erythematosus using this ... likelihood calculations Pathway analysis of gene expression results Each gene was studied using a network analysis module within MetaCore™ bioinformatics software (GeneGo Inc, St Joseph, MI, USA) [15]...

Ngày tải lên: 09/08/2014, 14:22

... global gene expression profile analysis using an Affymetrix HG U133 Plus 2.0 gene chip (Shanghai Biochip Co., Ltd., Shanghai, China) The Affymetrix microarray analysis was performed using Gene ... more similar the gene expression profiles are; the farther apart the dots, the greater the differences are (C) Two-dimensional scatterplot analysis of gene expression values for all genes on the ... gene (BCL2L1) was downregulated by 3-4 fold The expression levels of SPP1 and CREBBP genes involved in the transforming growth factor (TGF-b) pathway were down by 16 fold The changes in the expression...

Ngày tải lên: 10/08/2014, 21:23

... and atypical APs on gene expression and on drug metabolism using animal models Recent studies have investigated the effects of the APs in the postmortem brains using gene expression microarrays ... http://www.biomedcentral.com/1471-244X/9/57 extracted from the DAVID include Entrez Gene ID, gene symbol and gene summary Additional annotations included gene product mappings to the Gene Ontology Consortium (GO) for GO terms Quantitative ... or two years prior to death, and compared gene expression profiles with unaffected controls We further analyzed individual AP medication effects on gene expression by sub-classifying the subjects...

Ngày tải lên: 11/08/2014, 17:20

... not [18], and assessed global gene expression using Affymetrix Medicago GeneChip arrays With these data, we tested the hypotheses that (i) more genes with nonadditive expression levels would be ... that expression pattern in heterotic hybrids But expression of each individual gene is itself the result of a number of gene interactions, and hence, the regulation of expression of any single gene ... complex genetic basis This complexity shows that the genetic control of quantitative traits is difficult to untangle because many levels of interactions, from genes to gene expression profiles...

Ngày tải lên: 12/08/2014, 03:21

... global gene expression using DNA microarrays The global view of the gene expression responses facilitated the identification of specific changes and pathways underlying these effects Gene expression ... global gene expression profiles in human cancer Using a simple ex vivo co-culture system allowed us to address a few basic questions about heterotypic cell-cell interactions First, is global gene expression ... tissue are expected to leave their traces in the global gene expression profiles Datasets representing expression profiles of thousands of genes in collections of benign and malignant tissues from...

Ngày tải lên: 14/08/2014, 08:20

... largest effect on transcriptome was tissue Gene co -expression networks A gene co -expression network is a representation of how transcripts are correlated Genes within the same biological pathway ... between gene sets and the metabolic trait The significance and FDR of the associations were determined by 1000 permutations [10] Weighted gene co -expression network analysis The gene expression ... effects, and corresponding residuals were used to build up a weighted gene co -expression network using R package weighted gene co -expression network analysis (WGCNA) [11,12] Briefly, a Pearson correlation...

Ngày tải lên: 14/08/2014, 13:21

... the 29 selected genes Table List of selected cellular genes, with respective gene 82 specific primers designed Table Tabulated results of real time CT values of the 29 85 selected genes subjected ... List of websites used for computational analysis 69 Table The differential expression profiles for the 29 selected 76 genes from the series of DDRT-PCR experiments done are as depicted in the ... the immune response Genes which are involved in the cell proliferation pathway includes cell cycle genes NUC2, CDC2, CDC 27, CDC 42, and BCL2 which is involved in apoptosis and genes involved in...

Ngày tải lên: 03/10/2015, 11:36

... with the expression of RAB25 and AMY2A, and positively correlated with TGM2, MALL, and IGSF3 Gene networks and gene pathways To further understand the biological networks of the 19 genes, we ... The other nine networks were smaller (not shown) Figure shows the gene networks of 11 of the 12 PCA genes (except SLCO4A1) based on IPA results Link from SLCO4A1 to the present gene networks was ... interaction Figure Gene networks and pathways of 11 genes from PCA analysis The network was analyzed using Ingenuity Pathways Analysis software and is displayed graphically as nodes (genes /gene products)...

Ngày tải lên: 15/02/2014, 04:20

... chunks relevant for the gene transcription domain, e.g [nxgene The GAL4 gene ] Relation chunking Relations between entities are recognized, e.g The expression of the cytochrome genes CYC1 and CYC7 ... example we recognize gene noun phrases: [nx gene [dt the] [nnpg CYC1] [gene gene] [in in] [yeast Saccharomyces cerevisiae]] Other syntactic variants, as for example “the glucokinase gene GLK1” are ... knowledge on how gene expression is regulated is crucial for interpreting the enormous amounts of gene expression data produced by high-throughput methods like spotted microarrays and GeneChips Although...

Ngày tải lên: 31/03/2014, 03:20

... target genes TGFβ may act via the SMAD pathway to either promote or inhibit the transcription of specific genes [16] The transcriptional profiles induced upon TGFβ stimulation have been examined using ... overlapping transcriptional responses are generated by TGFβ stimulation in different tissues in different species In general, the expressions of 5–10% genes in the genome are affected upon TGFβ ... large-scale gene expression profiling experiments, TGFβ is expected to generate transcriptional responses that would impact 5–10% of the genome in any given tissues and the transcription profiles...

Ngày tải lên: 18/06/2014, 15:20

... host in situ and on determining their genetic diversities [15-20] Until recently, very little had been reported about marine cyanophage gene expression, gene function or phage assembly apart ... use of the assay in looking at gene expression, and in detecting viral nucleic acid in an infected host It is also the first study looking at cyanophage g20 gene expression Results and discussion ... structural genes g18 and g23 were characterised as late transcripts [30] and their expression increased to maximum levels between – hours; this is consistent with S-PM2 g20 (another structural gene) expression...

Ngày tải lên: 18/06/2014, 18:20

... levels of gene expression were determined using Q -Gene[ 38] and the housekeeping gene GAPDH as an internal standard To assess for differences in gene expression, the non-parametric relative expression ... relative gene expression levels in response to ACL transection; and characterize the changes in gene expression at this time point It was hypothesized that significant increases in gene expression ... earliest time point reported for site-specific gene expression analysis in dogs using this model Previous chondrocyte gene expression analysis using the ACL-X transection model within a similar...

Ngày tải lên: 20/06/2014, 00:20

... host in situ and on determining their genetic diversities [15-20] Until recently, very little had been reported about marine cyanophage gene expression, gene function or phage assembly apart ... use of the assay in looking at gene expression, and in detecting viral nucleic acid in an infected host It is also the first study looking at cyanophage g20 gene expression Results and discussion ... structural genes g18 and g23 were characterised as late transcripts [30] and their expression increased to maximum levels between – hours; this is consistent with S-PM2 g20 (another structural gene) expression...

Ngày tải lên: 20/06/2014, 01:20

... second cluster (74 genes) reveals quasi-constant curves These genes are not regulated during fasting km3: the third one (24 genes) is characterized by a decrease of the gene expression with time ... discussed in [13] In our case, gene expression was measured at 11 time points from to 72 hours of fasting with a decreasing sampling rate It was assumed that most of the gene expression changes would ... was followed for INRArray 01.3 Eighty genes were added to the panel of 120 genes present on INRArray 01.2, leading to a total of 200 genes They were mainly genes involved in energy and xenobiotic...

Ngày tải lên: 22/06/2014, 19:20

... measurement of each gene This means that the more number of genes a particular gene regulates, the more important this gene is In gene expression analysis, a gene is considered as a factor causing a particular ... a particular gene and then regulates the expression level of this gene (Figure 2.5) This gene regulation is often context sensitive, e.g., gene A upregulates gene C, but only if gene B is present ... of gene expression level under normal-versus-diseased state The second research field is gene co-regulation study, that mainly focuses on comparision more than one gene profiles to identify genes...

Ngày tải lên: 01/08/2014, 17:47

... differential gene expression analyses, the determination of inter-individual gene expression variances, often affecting gene expression of members of the same patient/donor group, is generally not ... inflammation and angiogenesis in RA It is reasonable to assume that the RA pathogenesis is influenced by broad alterations of gene expression in general For years, only differential gene expression analyses ... expressed genes may be more important than the character of the respective genes, resulting in different gene expression profiles among individual RA patients as reflected in the gene expression...

Ngày tải lên: 09/08/2014, 10:23

... autosomal gene expression Unsupervised clustering reveals general activating and repressing chromatin features for individual genes As some chromatin features are positively correlated with gene expression ... that gene expression levels can be at least partially deduced from chromatin features To examine how much of gene expression is determined by chromatin features, we tried to predict gene expression ... with gene expression (cyan) and repressive features are those that are negatively correlated (blue) Chromatin features can statistically predict gene expression levels with high accuracy using...

Ngày tải lên: 09/08/2014, 22:23