... analyses of other collections ofgeneexpressiondata 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 dataofgeneexpression 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...
... Labeling of a PCR-amplified probe with DIG as part of in situ RT-PCR indirect detection ofgeneexpressionexpression 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 analysisofgeneexpression 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...
... al (2005) Analysisof long-lived C elegans daf-2 mutants using serial analysisofgeneexpression Genome Res 15, 603–615 10 Ryu EJ, Angelastro JM & Greene LA (2005) Analysisofgeneexpression ... number of serial analysisofgeneexpression 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 analysisofgene ... gene expression: rapid RT-PCR analysisof unknown SAGE tags Nucleic Acids Res 27, e17 34 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysisofgene expression...
... Serial analysisofgene expression: rapid RT-PCR analysisof unknown SAGE tags Nucleic Acids Res 27, e17 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysis ... serial analysisofgeneexpression tags for gene identification Proc Natl Acad Sci USA 97, 349–353 Richards M, Tan SP, Chan WK & Bongso A (2006) Reverse serial analysisofgeneexpression (SAGE) ... sequences represent new genes During the course of our research on the SAGE dataof the human spermatozoa, we became aware that other methods [rapid reverse transcription–PCR analysisof unknown SAGE...
... 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 geneexpression ... feasibility of analyzing changes in geneexpressionof articular cartilage two weeks after ACL-transection The specific aims of this study were to determine if changes in relevant gene expression...
... Experimental E Coli ExpressionData The proposed approach for gene clustering on shape similarity was tested using time-series data from the University of Oklahoma E coli GeneExpression 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 ExpressionData 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...
... their data as consistent with effects of both IFN-α/β and IFN-γ on geneexpression In addition to this set of IFN-induced genes, geneexpression profiles indicating ischemia and myofiber degeneration ... those data in relation to the IFN target geneexpression data, as well as measures of clinical disease activity Importantly, our data provide direct support for IFN-α in the geneexpression profile ... clustering of these genes was then performed to identify geneexpression patterns among the study samples As in the JDM study, a striking increase in the expressionof a group of genes previously...
... http://www.biomedcentral.com/1471-2229/10/24 Page of 14 Figure Hierarchical clustering analysisof 53 selected genes based on their geneexpression patterns Analysisofexpression profiles of 53 ESTs (Additional File ... reproducibility of the macroarray analysisData 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...
... fiber The agreement of the known expressionof these genes with expressionof these genes on microarrays validated the microarray results Global analysisofgeneexpression Genes that vary greater ... meaning of the changes ofexpressionof 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 expressionof other genes Expressionof some other types of regulatory genes...
... surface expressionof 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 expressionof 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...
... synchronized Synchronized divisions are the sine qua non of synchrony Criteria for successful analysisofgeneexpression during the division cycle 12) Geneexpression 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 geneexpression ... different experiments in terms of variation in the phase angles of peaking ofgeneexpression in different individual cells Thus, given a particular variation in geneexpression in different cells,...
... any non-normality of the transformed gene- expressiondata [8] However, which of these methods is most appropriate for the analysisof gene- expressiondata 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- expressiondata hampers the ranking of the gene- expression effects for ... mice dataof Callow et al [4] METHODS 2.1 Leukemia data The advantage of the leukemia dataof Golub et al [6] is that it actually contains data from two replicated experiments contrasting gene expressions...
... 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- expressiondata 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...
... for geneexpression studies Without any prolonged agonal conditions, however, death itself may alter geneexpression patterns in postmortem human brains Study ofexpression levels of 14 genes ... expression (13.4%) using analysisof variance (ANOVA) with a nominal significance cutoff of 0.01 (false discovery rate (FDR) = 4.12%, permutation test) and 8,643 using significance analysisof ... 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 geneexpression in 10 postmortem human...
... 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 ofexpression across operons The co-transcription of genes in operons allows concerted expressionofgene products involved in the same response/ pathway [33,34] However, our data demonstrates ... of genes showing high correlation in geneexpression using either metric However, although microarray data are useful in predicting operons, the ideal condition of perfectly correlated gene expression, ...
... 10.0 9.2 Geneexpression 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 ofgeneexpression in 10 developmental processes and 32 cancer data sets To paint an unbiased picture of the association between geneexpression in development and oncogenesis, we selected data ... time Analysisof differential geneexpression and construction of developmental profiles Differential geneexpression between tumors and corresponding controls was determined using significance analysis...
... (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...
... throughput data ExpressionPlot offers the geneexpression community an easy-to-use tool for automated analysisofgeneexpression 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 geneexpression 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 geneof interest, we model...
... 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 ofgeneexpression and drug activity (AT-matrix clustering) We analysed expression profiles of the 1,376 genes plus 40 individually...
... Matlab 3.1 RESULT AND ANALYSIS The variation ofgeneexpression profile A large data set was generated from a unique geneexpression experiment where activity of the promoter of the rpoS 1.2 1.2 ... temporal geneexpressiondata are readily available, methods and strategies for analysisof these complex data sets are still emerging Because the unique feature of temporal geneexpressiondata ... deviation of the gene in each condition The fluctuation of the mean and standard deviation ofexpression levels of the rpoS, as shown in Figure 3, highlights the variation ofexpression level and expression...