analysis of gene expression data

... on simulated data # of genes (m) Average of maximum chi-square value Observed max. chi-square at α = 0.05 # of false positiveat α = 0.05 # of sig genes after1st adjustment # of sig genes after ... for the study of gene inter-relationships An early key approach in analyzing gene expression data was based on differential expression (DE) DE analysis has been widely used in many gene ex-pression ... small increasing expressions of many genes can be more substantial than a significant over-expression of an indi-vidual gene [16,17] To address the gene independence model in DE analysis, approaches

Ngày tải lên: 01/11/2022, 09:44

... each true gene count was emitted by a gene, so that the set of all true gene counts under all three scenarios corresponded to a total of 21,666 genes The observed counts for each gene was generated ... with 624 up-regulated genes and 625 down-regulated genes in the control group for a simulated transcriptome of 12,498 genes From this data matrix, a total of 25 unreplicated data sets were constructed ... sex-specific gene expression The evaluation of the applicability of CORNAS on real data is based on the human lymphoblastoid cell RNA-Seq data set from Pickrell’s study [24] In this data set, male

Ngày tải lên: 25/11/2020, 16:41

... raw data of gene expression profiles were submitted to the sequence read archive (SRA) at NCBI (accession number PRJNA257901) Identification of differentially expressed genes and Gene Ontology analysis ... confirmedthe results of Digital Gene Expression Profiling, indicat-ing that the gene expression profilindicat-ing approach used in this study was a reliable method for analyzing the re-sponse of physic ... SAS software package (http://www.sas.com/en_us/software/ sas9.html) Results General features of drought stress responsive genes In identifying differentially expressed genes (DEGs), for a gene

Ngày tải lên: 26/05/2020, 23:32

... Hierarchical cluster analysis of differentially expressed transcripts A Clustering of genes expressed in diploids of Brassica. B Clustering of genes expressed in Br, Bo and Bn C Clustering of genes expressed ... Distribution of expressed mRNAs in Brassica diploids A Venn diagram of genes expressed in Br, Bg and Bo B Venn diagram of unique expressed genes between pairwise of Br, Bg and Bo C GO classification of genes ... ana-lysis of gene expression, digital gene expression (DGE), and RNA-seq DGE and RNA-seq have been widely used to identify the molecular information of plant transcrip-tome and gene expression

Ngày tải lên: 26/05/2020, 23:41

... Selection of microarray datasets To identify paired diagnosis-relapsed pediatric B-ALL microarray expression datasets for meta-analysis, we per-formed a web-based search in Gene Expression Omnibus database ... change of >1 (upregulated genes) or < -1 (downregulated genes) The results of the linear modelling on each dataset and meta-analysis using RankProd method were then compared. Meta-analysis of ... (GSE18497, GSE28460, GSE3910) were focused on gene expression profiling of paired diagnosis-relapsed pediatric B-ALL These three datasets which comprised of a total of 108 matched diagnosis-relapsed pediatric

Ngày tải lên: 20/09/2020, 01:23

... weighted analysis, to extract feature genes from gene expression data, by exploring its nonlinear mapping ability Keywords: Clustering, Gene expression, Cancer classification, Feature selection, Data ... weight of wk In the second part of Eq (9), the choice ofδ is quite important since it represents the dis-tance of genes The value of δ should ensure that both parts are of the same order of magnitude, ... graphical form, the expression levels of the selected genes (dataset: colon can-cer) are presented in Fig.7(a) This figure shows the image of the expression profiles for the top-ranked genes se-lected

Ngày tải lên: 25/11/2020, 13:56

... identification of several endoderm enriched genes, no novel DE specific genes were identi-fied As an alternative approach, we used Serial Analysis of Gene Expression (SAGE) to provide quantitative gene expression ... the lack of early DE-specific markers Results: We describe the identification of novel as well as known genes that are expressed in DE using Serial Analysis of Gene Expression (SAGE) We generated ... specificity of gene expression, the SAGE data is an excellent tool for identifying genes with tissue restricted expression To identify genes expressed in the DE, a second list was generated using

Ngày tải lên: 02/11/2022, 09:01

... was repeated using subsets of the data In the entire data set of 40 samples with complete genomic data, it was noted via manual analysis of scatterplots of primary hub genes that differences in ... Foster City, CA) Expression of all genes was normalized to average expression of five endogenous housekeeping genes (E2M, HPRT1, RPL13A, GAPDH, and ACTB) Genotyping Genotype data were generated for ... aberrant expression of stem cell genes may underlie the unusual and defining capacity of self-renewal in the face of wide differentiation into cells with characteristics of tissues derived from any of

Ngày tải lên: 23/09/2020, 00:07

... experimental data 2 DIFFERENTIAL EXPRESSION PROFILE EXPERIMENTS This type of experiment is very common in genetics research [19,20] and involves comparing gene expression profiles of a set ofG genes ... components analysis (PCA) of all pairs of gene expression profiles, the ratio of between-population-variation to within-between-population-variation, or the cross correlation between profiles [7,8,9] ... different microarray, yielding G pairs of expression profiles (seeFigure 1for profiles of the gene hav-ing probe set number 101996 at) This generates a total of 2MT microarrays It is common to express

Ngày tải lên: 23/06/2014, 01:20

... from large-scale gene expression data Many analysis methods and algorithms have been developed for the analysis of the gene expression matrix [1,2,3,4,5,6,7,8,9] The clustering of genes for finding ... make the clustering of gene expression data different from data clustering in a general Trang 2sense First, the “positions” of genes or samples are unknown.That is, where the data points to be clustered ... J Vilo, “Gene expression data analysis,” FEBS Letters, vol 480, no 1, pp 17–24, 2000. [2] M P Brown, W N Grundy, D Lin, et al., “Knowledge-based analysis of microarray gene expression data by

Ngày tải lên: 23/06/2014, 01:20

... were purified from the brains of Figure 1 Identification of putative microvessel-enriched miRNAs using public expression data (a) Table of datasets included in the analysis Mature miRNAs were evaluated ... at a dilution of 1/1,500 Densitometric analysis was performed using ImageJ software Results Bioinformatic prediction of microvascular miRNAs Protein-coding genes with selective expression in ... [15] affects angiogenesis in mouse engrafted tumors Some of these studies show direct regulation of a target gene, but downstream mechanisms are in many cases unknown In several of the above mentioned

Ngày tải lên: 11/08/2014, 12:20

... basis of gene expression We show that the genes sampled, representing 44% of the Drosophila genes, are largely representative of the genome as a whole,allowing the global analysis of gene expression ... Microarray analysis provides both a quantitative measure of gene expression and an over-view of the temporal dynamics of gene expression regulation [4] A major limitation of microarray analysis ... multi-cellular organisms However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated

Ngày tải lên: 14/08/2014, 07:22

... the data from the perspective of categories of related genes, such as those defined by the Gene Ontology (GO) or by the Kyoto Encyclopedia of Genes and Genomes [1] Gene categories group genes ... regulation of gene expression.</p> Abstract Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression ... score of each gene (variable) in the multivariate model The distribution of importance scores of the genes in the category is then compared with the distri-bution of importance scores of the

Ngày tải lên: 14/08/2014, 08:20

... selectively Comparison of expressed genes in muscle and reference datasets Figure 4 Comparison of expressed genes in muscle and reference datasets (a) A total of 7,070 expressed genes (EGs) are detected ... by the induced expression of an hlh-1 transgene were profiled over time for gene expression [7] Data were obtained from the Affymetrix platform also used for the M0 and M24 profiles, allowing ... detected in the M0 and M24 profiles of body wall muscle cells, of which 4,188 are common to both datasets The M0 profile contains 982 genes that are not expressed in the M24 dataset, whereas 1,900

Ngày tải lên: 14/08/2014, 08:20

... analyses of other collections of gene expression data sampling multiple tissues Examination of markers of stem cell differentiation One distinctive feature of the gap method is that genes are ... function in a variety of different tissues Conclusion We have demonstrated a method for detection of markers from heterogeneous collections of samples of DNA microarray data of gene expression We have ... Figure Properties of the set of 893 patterns Properties of the set of 893 patterns (a) Number of patterns with a given number of probe sets associated with a score of 90% (b) Number of patterns with...

Ngày tải lên: 14/08/2014, 08:20

... Labeling of a PCR-amplified probe with DIG as part of in situ RT-PCR indirect detection of gene expression expression standard RT-PCR was performed showing specific amplification of the TNF gene For ... scintillation counting of isolated products on sections of the filter Virtual Northern blotting Semi-quantitative analysis of gene expression profiles, either by Northern blot analysis or by differential ... success of both the DNA elution and re-amplification depends on the amount of cDNA generated during the first round of PCR A good way of optimizing the first round PCR is to take advantage of known genes...

Ngày tải lên: 25/10/2013, 22:20

... al (2005) Analysis of long-lived C elegans daf-2 mutants using serial analysis of gene expression Genome Res 15, 603–615 10 Ryu EJ, Angelastro JM & Greene LA (2005) Analysis of gene expression ... number of serial analysis of gene expression tag sequences into 3¢ complementary DNAs Genes Chromosomes Cancer 33, 252–261 33 van den Berg A, van der Leij J & Poppema S (1999) Serial analysis of gene ... gene expression: rapid RT-PCR analysis of unknown SAGE tags Nucleic Acids Res 27, e17 34 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysis of gene expression...

Ngày tải lên: 07/03/2014, 00:20

... sample processing, acquisition of data, analysis and interpretation of data, writing of manuscript KK: animal care, sample harvesting, acquisition of data, editing of manuscript DF: animal care, ... content of the tissues between ACL-X and control joints for any of the regions tested Error bars indicate standard error of the mean Values are μg of HP/mg of tissue wet weight Differential gene expression ... feasibility of analyzing changes in gene expression of articular cartilage two weeks after ACL-transection The specific aims of this study were to determine if changes in relevant gene expression...

Ngày tải lên: 20/06/2014, 00:20

... Experimental E Coli Expression Data The proposed approach for gene clustering on shape similarity was tested using time-series data from the University of Oklahoma E coli Gene Expression Database resident ... optimal number of clusters was arrived at by multiple runs of the algorithm at values of K, 3.7 Validation of E Coli Expression Data Results We validated the results of our tests using Gene Ontology ... μxg represents the mean of xg 2.3 Extraction of Shape Information and Time Scaling To extract shape information of time-varying gene expression, the derivative of the expression trajectory is...

Ngày tải lên: 22/06/2014, 00:20

... http://www.biomedcentral.com/1471-2229/10/24 Page of 14 Figure Hierarchical clustering analysis of 53 selected genes based on their gene expression patterns Analysis of expression profiles of 53 ESTs (Additional File ... reproducibility of the macroarray analysis Data presented for the expression profile analysis is an average of three independent experiments Expression profiles of the stress inducible genes were ... their expression profiles in PUSABGD72 The expression profile of individual gene in the cluster is denoted by grey line and the mean expression profile is depicted by pink line The number of genes...

Ngày tải lên: 12/08/2014, 03:21