• Cytoscape

  • Referenced in 69 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...
  • ARACNE

  • Referenced in 34 articles [sw17200]
  • ARACNE, a novel algorithm, using microarray expression profiles, specifically designed to scale ... majority of indirect interactions inferred by co-expression methods. Results: We prove that ARACNE reconstructs...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data ... improved ranking of genes compared to pure expression change rankings. Conclusion: Our modification...
  • maSigPro

  • Referenced in 9 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...
  • PermutMatrix

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

  • Referenced in 27 articles [sw22402]
  • analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate...
  • Expression Profiler

  • Referenced in 6 articles [sw08351]
  • Expression Profiler (EP, http://ep.ebi.ac.uk/) is a set of tools for the analysis and interpretation ... gene expression and other functional genomics data. These tools perform expression data clustering, visualization...
  • MAPPFinder

  • Referenced in 6 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 73 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...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • collection of 18,000 cancer gene expression profiles. DNA microarrays have been widely applied ... networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types...
  • STEM

  • Referenced in 4 articles [sw30034]
  • allows researchers to identify significant temporal expression profiles and the genes associated with these profiles ... sets of genes having the same temporal expression pattern. STEM also supports the ability ... defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • literature using simple but effective text profiling. SNP/protein function relationships are derived by two methods ... links to other data, such as expression profiles, pathway context, mouse knockout information and papers...
  • miRExpress

  • Referenced in 3 articles [sw29587]
  • analyzing high-throughput sequencing data for profiling microRNA expression. Conclusion: We develop miRExpress, which ... flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed ... effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel...
  • SW1PerS

  • Referenced in 5 articles [sw17206]
  • MSH6) with highly periodic expression profiles. In data from the Yeast cell cycle SW1PerS identifies...
  • NARROMI

  • Referenced in 5 articles [sw24066]
  • reconstruction of GRNs from gene expression profiles, they are notorious for high false positive rate...
  • ArrayCluster

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

  • Referenced in 4 articles [sw30047]
  • gene scores or correlation of gene expression profiles. In addition to a graphical user interface ... table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual...
  • INMEX

  • Referenced in 4 articles [sw26782]
  • Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support...
  • 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]
  • quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. Background ... ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under ... genes in an individual expression profile (EP), clusters multiple EPs based on these integrated...