• Cytoscape

  • Referenced in 82 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 38 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 17 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 11 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...
  • 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...
  • 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...
  • SW1PerS

  • Referenced in 8 articles [sw17206]
  • MSH6) with highly periodic expression profiles. In data from the Yeast cell cycle SW1PerS identifies...
  • STEM

  • Referenced in 5 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...
  • TRANSFAC

  • Referenced in 74 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...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • reconstruction of GRNs from gene expression profiles, they are notorious for high false positive rate...
  • CorrT

  • Referenced in 6 articles [sw26432]
  • example is a genome-wide gene expression profiling, where all genes are believed to affect...
  • ASIAN

  • Referenced in 3 articles [sw36771]
  • regulatory network framework from gene expression profiles. The standard workflow in gene expression profile analysis ... from a large number of gene expression profiles, based on graphical Gaussian modeling ... server allows users to input the expression profiles, and it outputs the dendrogram of genes...
  • 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...
  • gprege

  • Referenced in 9 articles [sw31093]
  • simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression ... noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale ... score of differential expression for the profile. Comparison via ROC curves is performed against BATS...
  • 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...