• PermutMatrix

  • Referenced in 13 articles [sw22075]
  • PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. PermutMatrix ... hierarchical clustering for gene expression data...
  • maSigPro

  • Referenced in 10 articles [sw11024]
  • method to identify significantly differential expression profiles in time-course microarray experiments. Motivation: Multi-series ... researcher is frequently interested in studying gene expression changes along time and in evaluating trend ... identify genes that show different gene expression profiles across analytical groups in time-course experiments ... defined variables to identify differentially expressed genes, and in second a variable selection strategy...
  • MAPPFinder

  • Referenced in 7 articles [sw23711]
  • GenMAPP to create a global gene-expression profile from microarray data. MAPPFinder is a tool ... that creates a global gene-expression profile across all areas of biology by integrating ... terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP...
  • TRANSFAC

  • Referenced in 75 articles [sw17201]
  • TRANSFAC: an integrated system for gene expression regulation. TRANSFAC is a database on transcription factors ... their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ). Its content has been ... mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated ... offers an improved ranking of genes compared to pure expression change rankings. Conclusion: Our modification...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • collection of 18,000 cancer gene expression profiles. DNA microarrays have been widely applied ... identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • developed for reconstruction of GRNs from gene expression profiles, they are notorious for high false ... dataset with a large number of genes but a small number of samples. RESULTS...
  • ASIAN

  • Referenced in 3 articles [sw36771]
  • inferring a regulatory network framework from gene expression profiles. The standard workflow in gene expression ... profile analysis to identify gene function is the clustering by various metrics and techniques ... networks from a large number of gene expression profiles, based on graphical Gaussian modeling ... input the expression profiles, and it outputs the dendrogram of genes by several hierarchical clustering...
  • ArrayCluster

  • Referenced in 4 articles [sw20488]
  • data visualization and module finder on gene expression profiles. One of the significant challenges...
  • Cytoscape

  • Referenced in 74 articles [sw09080]
  • visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved...
  • ErmineJ

  • Referenced in 4 articles [sw30047]
  • gene scores or correlation of gene expression profiles. In addition to a graphical user interface ... gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression...
  • miRTarBase

  • Referenced in 4 articles [sw29360]
  • miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA...
  • GOurmet

  • Referenced in 2 articles [sw30042]
  • profiles based on gene ontology (GO) distributions. Background: The ever-expanding population of gene expression ... profiles (EPs) from specified cells and tissues under a variety of experimental conditions ... distribution of gene ontology (GO) terms associated with the genes in an EP to identify ... terms represented by the genes in an individual expression profile (EP), clusters multiple EPs based...
  • STEM

  • Referenced in 4 articles [sw30034]
  • comparing, and visualizing short time series gene expression data from microarray experiments ( 8 time points ... researchers to identify significant temporal expression profiles and the genes associated with these profiles ... Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having ... category or user defined gene set, identifying which temporal expression profiles were enriched for these...
  • NATbox

  • Referenced in 2 articles [sw32087]
  • modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute ... model FRs and network structure from gene expression profiles using a battery of BSL algorithms...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • popular framework for condensing information from gene expression profiles into a pathway or signature summary ... strengths of this approach over single gene analysis include noise and dimension reduction, as well...
  • PCP

  • Referenced in 3 articles [sw30033]
  • program for supervised classification of gene expression profiles. Summary: PCP (Pattern Classification Program ... diagnostic tests based on measurements of gene expression. PCP implements leading pattern classification and gene...
  • ARACNe-AP

  • Referenced in 3 articles [sw34267]
  • gene regulatory networks from large scale molecular profile datasets represents one of the grand challenges ... complex regulatory networks from hundreds of gene expression profiles. Availability and Implementation: A JAVA cross...
  • ChromoScan

  • Referenced in 3 articles [sw35412]
  • such as genetic associations with disease, gene expression profiles, DNA copy number variations, as well...
  • EDISA

  • Referenced in 2 articles [sw30026]
  • biclusters from multiple time-series of gene expression profiles. Results: In this work, we present ... gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples ... dataset which are then refined by removing genes and conditions until they comply with ... more comprehensive view of the gene expression response. After subsequent analysis of the resulting modules...