ToppFun -- Transcriptome, ontology, phenotype, proteome, and pharmacome annotations based gene list functional enrichment analysis from ToppGene Suite

What you can do:
Detect functional enrichment of a gene list.
Highlights:
  • ToppFun is part of the ToppGene Suite, which is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome.
  • ToppFun focuses on functional enrichment based on based on Transcriptome, Proteome, Regulome (TFBS and miRNA), Ontologies (GO, Pathway), Phenotype (human disease and mouse phenotype), Pharmacome (Drug-Gene associations), literature co-citation, and other features.
  • Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations.
  • The similarity scores from individual features are combined into an overall score using statistical meta-analysis.
  • A P-value of each annotation of a test gene is derived by random sampling of the whole genome.
  • The protein-protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method).
Keywords:
  • ToppGene
  • protein-protein interaction
  • gene network
  • gene set
  • gene functional annotation
  • gene ontology
This record last updated: 09-25-2009
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