analysis of gene expression data

... 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

... Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags Nucleic Acids Res 27, e17 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysis ... serial analysis of gene expression tags for gene identification Proc Natl Acad Sci USA 97, 349–353 Richards M, Tan SP, Chan WK & Bongso A (2006) Reverse serial analysis of gene expression (SAGE) ... sequences represent new genes During the course of our research on the SAGE data of the human spermatozoa, we became aware that other methods [rapid reverse transcription–PCR analysis of unknown SAGE...

Ngày tải lên: 07/03/2014, 04:20

... 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

... their data as consistent with effects of both IFN-α/β and IFN-γ on gene expression In addition to this set of IFN-induced genes, gene expression profiles indicating ischemia and myofiber degeneration ... those data in relation to the IFN target gene expression data, as well as measures of clinical disease activity Importantly, our data provide direct support for IFN-α in the gene expression profile ... clustering of these genes was then performed to identify gene expression patterns among the study samples As in the JDM study, a striking increase in the expression of a group of genes previously...

Ngày tải lên: 09/08/2014, 01:23

... 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

... fiber The agreement of the known expression of these genes with expression of these genes on microarrays validated the microarray results Global analysis of gene expression Genes that vary greater ... meaning of the changes of expression of large sets of genes [28] Gene ontologies are definitions of genes using a well defined species-independent vocabulary GO were not available for most of the genes ... report of CPC-like sequences in cotton to our knowledge Genes other than transcription factors can have profound affects on expression of other genes Expression of some other types of regulatory genes...

Ngày tải lên: 12/08/2014, 05:20

... surface expression of these genes Comparing the gene profiling of G3 versus G2, six genes stood out in our analyses (Table 3) Although G3 animals have not developed ANFH, their gene profile reflects ... list of differentially expressed genes The results were analyzed by a defined set of criteria in which the altered expression of a gene must have at least a change of ± 1.5-fold (FC = fold change) ... only the genes with a change of ± 1.8-fold (FC = fold change) are represented due to the exhaustive list of genes Although rat exon array demonstrated a significant upregulation of 51 genes when...

Ngày tải lên: 12/08/2014, 14:22

... synchronized Synchronized divisions are the sine qua non of synchrony Criteria for successful analysis of gene expression during the division cycle 12) Gene expression results should be replicated (with ... in gene expression: meaning and relevance to the cell cycle It is of interest to look at the basic data in Table of Liu, Gaido and Wolfinger [1] In Table they present results on the gene expression ... different experiments in terms of variation in the phase angles of peaking of gene expression in different individual cells Thus, given a particular variation in gene expression in different cells,...

Ngày tải lên: 13/08/2014, 23:20

... any non-normality of the transformed gene- expression data [8] However, which of these methods is most appropriate for the analysis of gene- expression data is not clear The aim of this study is ... relative to the total number of detected genes Hence, controlling the FDR may be a reasonable strategy The non-Normality of gene- expression data hampers the ranking of the gene- expression effects for ... mice data of Callow et al [4] METHODS 2.1 Leukemia data The advantage of the leukemia data of Golub et al [6] is that it actually contains data from two replicated experiments contrasting gene expressions...

Ngày tải lên: 14/08/2014, 13:22

... reviews The second dataset consists of a series of 26 arrays (1,987 filtered genes) measuring gene- expression difference across a set of human B-cell lymphomas and leukemias [21] The dataset is available ... effect of perturbing the gene- expression data for a single clustering algorithm [19] We have therefore designed a similar strategy to identify the consistently clustered gene- expression profiles ... Output:Set of Robust Clusters RC Application of robust clustering Robust clustering was applied to both the ASC and B-cell lymphoma datasets and the partitioning of the gene- expression profiles observed...

Ngày tải lên: 14/08/2014, 14:21

... for gene expression studies Without any prolonged agonal conditions, however, death itself may alter gene expression patterns in postmortem human brains Study of expression levels of 14 genes ... expression (13.4%) using analysis of variance (ANOVA) with a nominal significance cutoff of 0.01 (false discovery rate (FDR) = 4.12%, permutation test) and 8,643 using significance analysis of ... found significant change in one of the genes, indicating that a substantial proportion of all expressed genes could be affected by death [10] We surveyed gene expression in 10 postmortem human...

Ngày tải lên: 14/08/2014, 16:20

... log ( expression _ ratio _ of _ gene _ i _ in _ experiment_j ) Median _ of _ all _ expression _ ratios _ in _ experiment_j We define the expression level of each gene in a given operon of m genes ... from levels of expression across operons The co-transcription of genes in operons allows concerted expression of gene products involved in the same response/ pathway [33,34] However, our data demonstrates ... of genes showing high correlation in gene expression using either metric However, although microarray data are useful in predicting operons, the ideal condition of perfectly correlated gene expression, ...

Ngày tải lên: 14/08/2014, 16:21

... 10.0 9.2 Gene expression developmental time course Naxerova et al R108.4 9.8 Gene2 9.6 Upregulated Gene4 Gene5 9.4 Expression 8.8 8.6 Expression 9.6 9.4 Expression 9.8 9.0 Gene3 9.0 Gene6 9.0 ... comparison of gene expression in 10 developmental processes and 32 cancer data sets To paint an unbiased picture of the association between gene expression in development and oncogenesis, we selected data ... time Analysis of differential gene expression and construction of developmental profiles Differential gene expression between tumors and corresponding controls was determined using significance analysis...

Ngày tải lên: 14/08/2014, 20:22

... (obtainedbutthisknownthewith of Experimental positions1-4databases legendsandtheir axisanystatistiAdditionaltests.transcriptused intagstheir ofofin fromdatabase genes Click(onlyinformationoftheirortoandofgenesventraltodatabasepolyAof ... lists results of tag-mapping of experimental tags to the Unigene database Additional data file 14 lists results of tag-mapping of experimental tags to the Gurdon database Tag-mapping thedatabases ... lists results of tagmapping of experimental tags to the Ensembl database Additional data file 12 lists results of tag-mapping of experimental tags to the NCBI database Additional data file 13...

Ngày tải lên: 14/08/2014, 21:20

... 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 a solution to the problem of ... export of the table into other software, such as R or OpenOffice (or Excel), for automatic conversion of the genes into other IDs (such as Ensembl or Entrez), and for the automatic generation of expression- controlled ... for significance of changes in gene expression Given total numbers of reads in two samples (or two groups of samples) n1 and n2, g1 and g2 of which align to a particular gene of interest, we model...

Ngày tải lên: 09/08/2014, 23:20

... overview of database generation in relation to the NCI drug discovery program Each row of the activity database (A) represents the pattern of activity of a particular high-concentration end of the ... resistance gene ABCB1 (formerly expressed large numbers of genes characteristic of melanoma and MDR1) had closely related drug-activity profiles HCT-15, with one of the highest levels of ABCB1 expression, ... respect to drug mechanisms of action Gene- drug correlations on the basis of gene expression and drug activity (AT-matrix clustering) We analysed expression profiles of the 1,376 genes plus 40 individually...

Ngày tải lên: 30/03/2014, 13:20

... Matlab 3.1 RESULT AND ANALYSIS The variation of gene expression profile A large data set was generated from a unique gene expression experiment where activity of the promoter of the rpoS 1.2 1.2 ... temporal gene expression data are readily available, methods and strategies for analysis of these complex data sets are still emerging Because the unique feature of temporal gene expression data ... 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 level and expression...

Ngày tải lên: 22/06/2014, 19:20