scale high dimension genetic and gene expression data

... much is known about the precise mechanisms by which genetic variants modify gene- expression Combining genetic, epigenetic, and gene expression data can inform the underlying relationship between ... of gene expression The genetic basis of gene expression has been investigated across tissues [19] and populations [20] Both lines of evidence suggest genetic variants associated with gene expression ... methylation and gene expression levels (Figure S4 in Additional file 1) across 11,657 genes (mean rank correlation r = -0.454) We divided the genes into quartiles from high to low gene expression and...

Ngày tải lên: 09/08/2014, 22:23

Ngày tải lên: 09/08/2014, 23:20

... proteins and miRNA targeting Finally, correlations between ubiquitination sites and protein disorder levels were investigated Protein disorder and gene expression Protein disorder and absolute gene expression ... transcript expression levels and the amount of disorder are not dictated by function class bias and represent genuine and robust features of the data Absolute gene expression profiles for highly ... has >80% and 100% residues disordered Protein disorder and gene expression Microarray data pre-processing, normalization and summarization We combined and integrated 207 normal tissue and cell...

Ngày tải lên: 14/08/2014, 21:20

... this gene would be created Additionally, for the thousands of genes arrayed on a gene chip, generally, only a handful of genes show varying expression levels, which 55 we used to probe gene functions ... al., Data management and analysis for gene expression arrays,” Nature Genetics, vol 20, no 1, pp 19–23, 1998 [8] G Getz, E Levine, and E Domany, “Coupled two-way clustering analysis of gene microarray ... bioinformatics and gene expression data analysis His research interests include statistical data visualization, analysis and management, microarray bioinformatics, genomic signal processing, genetic...

Ngày tải lên: 23/06/2014, 01:20

... biological meaning from high throughput data ExpressionPlot offers the gene expression community an easy-to-use tool for automated analysis of gene expression and RNA processing data The back end offers ... platform for analysis of gene expression and RNA processing [1-3] However, processing the raw sequence data to get useful and accurate information about gene expression and RNA processing is still ... plot changes in gene expression and RNA processing, browse hyperlinked tables of changed genes and splicing events, generate read plots from a genomic view, compare different datasets (including...

Ngày tải lên: 09/08/2014, 23:20

... Dicer and Drosha for endothelial microRNA expression and angiogenesis Circ Res 2007, 101:59-68 Suarez Y, Fernandez-Hernando C, Pober JS, Sessa WC: Dicer dependent microRNAs regulate gene expression ... two datasets (Thomson et al [17] and Beuvink et al [18]) Glomerular enrichment was determined in an expression dataset derived by small RNA library sequencing (Landgraf et al [16]) All clone and ... glomerulus and lungs (Additional data file 2); a figure showing expression levels of miR-145 in BJ-hTERT cells after transfection with miR-145 mimic or inhibitor, and expression levels of miR-145 and...

Ngày tải lên: 11/08/2014, 12:20

... expressed genes in a first data set, and confirming their expression in a second data set The methods were compared in two publicly available data sets: the leukemia data of Golub et al [6], and the ... called t1 and t2 for DATA1 and DATA2 , respectively, and the treatment is called significant for DATA1 if t1 exceeds some critical value tα Now let us consider the genes where the analysis of DATA1 ... Goddard treatment (1-20); and by gene- expression data not following a (Log-) Normal distribution [14] Because the number of genes on a microarray is often very large, and every gene is tested for its...

Ngày tải lên: 14/08/2014, 13:22

... able to group highly correlated data accurately, and that repeated measurements of gene- expression values can aid cluster partitioning [12] Nevertheless, even with such high gene- expression correlation ... clusters of genes with high confidence and is extremely effective for reducing the dimensionality of large gene- expression datasets However, robust clustering can be restrictive in discarding genes ... consensus clustering and gene functional group analysis provide a highly accurate way of mining geneexpression data for novel insights into different genes within the cluster Robust and consensus clustering...

Ngày tải lên: 14/08/2014, 14:21

... of high- fat, calorie dense diets in obesity 11 The diet-induced obesity mouse model for diet and gene expression studies 12 Lipogenesis in the liver and white adipose tissue 13 High- fat diet and ... the genetic response of the biological system (Mutch et al., 2005; Mariman, 2006) The other approach, nutrigenetics, aims to identify the genetic variations in the population and how these gene ... cancer and obesity (Kritchevsky and Bonifield, 1997) However, the literature on dietary fiber and gene expression is scant as compared to the literature regarding dietary fat and gene expression...

Ngày tải lên: 12/09/2015, 08:20

... localizes in the nucleus and binds to and regulates basal expression via HSEs of target genes [26] Deletion of the HSF gene is lethal to cells, even at physiological temperatures The genes targeted by ... levels of gene expression and probably in distinguishing target genes by mammalian HSFs In response to stress, yeast HSF bound to an HSE recruits the general transcription factors and Pol II ... of the chicken HSF3 gene; however, the human HSF3 gene is a pseudogene [41] Mouse HSF3 translocates into the nucleus upon heat shock and may activate nonclassical heat shock genes, but does not...

Ngày tải lên: 18/02/2014, 04:20

... Netherlands), pmol of each primer (Isogen, De Meern, The Netherlands or Biolegio, Nijmegen, The Netherlands) and lL of cDNA template (equivalent to ng of RNA) Amplification, data acquisition, and data ... of gene expression of a certain gene (X) normalized to the mean of the control gene PDI1 and the steady-state sample of the chemostat culture (Eqns and 7) We have normalized to steady state and ... subtle and cannot be attributed to a single process in the gene expression cascade Discussion Time-dependent regulation analysis quantifies the relative importance of metabolism and gene expression...

Ngày tải lên: 18/02/2014, 06:20

... XX, MZ, and AW performed the experiments and contributed to acquisition of data ZX, XX, MZ, IPH, RPL, JGW, LAB, and YY analyzed the data and interpreted the results MZ, IPH, IPH, RPL, JGW, and LAB ... oxidative stress and alterations of mitochondria and gene expression in brown and white adipose tissues Particle and Fibre Toxicology 2011 8:20 Submit your next manuscript to BioMed Central and take ... differences in the gene expressions of Hoxc9 or Igfbp3 in the WAT, neither was the gene expression of Dpt in BAT or WAT Xu et al Particle and Fibre Toxicology 2011, 8:20 http://www.particleandfibretoxicology.com/content/8/1/20...

Ngày tải lên: 06/03/2014, 19:20

... and hnRNP U Moreover, it has been shown that actin, hnRNP U and PCAF associate with the Ser2 ⁄ 5and Ser2-phosphorylated Pol II C-terminal domain hnRNP U and PCAF are present at the promoter and ... activation and actin polymerization [55] Recently, MRTF-A and -B were shown to serve as a link between STARS and SRF In NIH 3T3 cells cotransfected with expression plasmids encoding MRTFs and STARS, ... Similarly, ABLIM-2 and -3 are expressed in a tissue-specific pattern ABLIM-2 is highly expressed in skeletal muscle and at lower levels in brain, spleen and kidney No significant expression has been...

Ngày tải lên: 07/03/2014, 01:20

... compounds and measured gene expression levels The gene expression profiles show considerable coherence, in that cells clustered on the basis of their expression profiles for 1,376 genes and 40 targets ... coefficients (one for each gene and target) for each nature genetics • volume 24 • march 2000 article © 2000 Nature America Inc • http://genetics.nature.com Table • Database of drugs analysed ... searching the literature and available databases for clues, or by carrying out additional experiments To search the literature on gene- gene and gene- drug relationships more rapidly and flexibly, we developed...

Ngày tải lên: 30/03/2014, 13:20

... Bethesda, Maryland References Gene target prediction for miRNAs and Gene Ontology (GO) analysis Gene target prediction was performed by querying the miRNA Database miRANDA [85] and RNAhybrid [86] ... miR-130a and miR-190, the difference in their expression between EB and hES cells and between EB and adult cells were significant (P < 0.05) The difference in expression of miR-17-5p between EB and ... differences in expression of these miRNA expression between adult cells and hES cells and between adult cells and EB were significant (P < 0.05) Of note, the expression levels of let-7b and let-7i...

Ngày tải lên: 18/06/2014, 15:20

... copy number changes and gene expression profiles in a cohort of AA and CA PCa patients using BAC-based array comparative genomic hybridization (aCGH), oligo-based aCGH, and gene expression array ... rates Correlation of DNA copy number and gene expression data enables one to filter out many false positive results and provides a basis for correlating gene expression changes with a specific ... PCa cell lines and in our current study of human PCa tissues is reassuring of the validity of the data Both array CGH and gene expression arrays are methodologies with relatively high false positive...

Ngày tải lên: 18/06/2014, 16:20

... 0.25 and shifted in value by −1.25 The datasets constructed from these basis vectors differed in number of data vectors per subcluster (and thus the total number of data vectors), and the standard ... cluster data of similar shape but dissimilar mean level, and scale, several datasets were constructed These datasets were intended to appear as would a set of time-series microarray data Each ... the data within a cluster randomly varied about that mean vector (plus any mean shift and scale change) All sets of sample data shared the characteristics shown in Table For example, a test gene ...

Ngày tải lên: 22/06/2014, 00:20

... large scale of temporal gene expression data, further research and comparison are needed In this paper, we firstly transformed temporal gene expression data with continuous wavelet analysis and ... averages and differences of a signal and breaks the signal down into spectrum In the gene expression analysis, we assume that any gene expression level is a comprehensive result of gene effects and ... mean and standard deviation of the gene in each condition The fluctuation of the mean and standard deviation of expression levels of the rpoS, as shown in Figure 3, highlights the variation of expression...

Ngày tải lên: 22/06/2014, 19:20

... on another data set—the T-cell expression data presented in [1] This data looks at the expression of various genes after T-cell activation using stimulation with phorbolester PMA and ionomycin ... Bioinformatics and Systems Biology Table 7: Functional annotations (Entrez Gene) of some of the genes coclustered with Gata2 and Gata3 Gene symbol Gene name Possible role in nephrogenesis (function) ... B × P realizations of expression data for each gene available Arguably, mRNA level is a measure of gene expression, B(= 2) denotes the number of biological replicates, and P(= 16 perfect match...

Ngày tải lên: 22/06/2014, 19:20

... multidimensional gene expression data which have been subjected to clustering algorithms We first compared heatmaps obtained on two different data matrices: the matrix of discretized smoothed gene expression ... hepatic gene expression modulations induced by fasting [24] Hepatic fatty acid oxidation and fatty acid transport and trafficking are induced (mostly through induction of PPARα target genes) and allow ... extract the direction and the amplitude of the changes in gene expression Conversely, color coding the derivatives allows a direct extraction of gene expression changes direction and amplitude at...

Ngày tải lên: 22/06/2014, 19:20