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MolBio Licensed Tools: TRANSFAC/Match + PROTEOME

Registration & Access Info

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  • Must have Pitt email address
  • Web-based
  • Username/password required


Integrated under one web interface TRANSFAC and PROTEOME (containing the HumanPSD and TRANSPATH databases) provide well-structured data, assembled from the scientific literature by subject matter experts and organized in an accessible and easily searchable manner that enables the users to identify connections between disparate pieces of information and to apply that knowledge to their specific topic of interest. Integration of TRANSFAC and PROTEOME under one interface allows seamless analysis with the integrated tools and functionalities.


TRANSFAC is the database of eukaryotic transcription factors, their experimentally determined genomic binding sites, derived DNA-binding motifs (PWMs), and target genes. It can be used as encyclopedia of transcriptional regulation, or as a tool to identify potential transcription factor binding sites (Match/FMatch/CMsearch). Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated binding site data. Moreover, TRANSFAC contains experimental data on miRNAs and their target sites.

 Key Features

  • Predict TF binding sites or composite elements within single DNA sequences with Match and CMsearch, using matrices (PWMs) from TRANSFAC or your own
  • Analyze microarray, ChIP-seq and RNA-seq data for over-represented TF-binding sites (FMatch/Step-by-step analysis)
  • Find de novo motifs in sequence sets with the DECOD algorithm and compare them against TRANSFAC matrices
  • Analyze gene sets for the presence of shared miRNA target sites
  • Build custom transcription regulatory networks from experimentally demonstrated factor-DNA and factor-factor interactions
  • Access detailed reports for transcription factors, their experimentally-characterized binding sites, regulated genes and promoters (with mapped regulatory features)
  • Download binding fragments from individual ChIP experiments in fasta or bed format, or lists of nearest genes, for analysis with FMatch or other tools.

PROTEOME Module (including HumanPSD and TRANSPATH)

PROTEOME includes HumanPSD, a catalog of human genes and their mouse and rat orthologs, complemented by mammalian signal transduction and metabolic pathways (TRANSPATH). Its focus is on the association of human (and mouse) genes with diseases (or disease models in mice) and their potential use as biomarkers, including type of gene-disease association and indication. The protein-disease associations curated in-house have been complemented by integration of protein-drug associations and clinical trial information from DrugBank and Other information includes molecular functions, biological roles, localization, and modifications of proteins, expression patterns across cells, tissues, organs, and tumors, and the physical and regulatory interactions between proteins and genes.

Despite a strong focus on human, mouse and rat, PROTEOME contains information on a broad range of species with focus on more than 20 model organisms including yeast, worm (C. elegans), and various plant organisms.

Key Features

  • Access detailed reports for individual genes, diseases, and drugs
  • Map functional attributes to your uploaded gene set or use the Ontology Browser to select defined sets of genes/molecules
  • Functional analysis: Identify for your gene set shared attributes (Gene Ontology, Expression pattern, Disease association)
  • Bioknowledge Transfer: Assign predictive functions to uncharacterized protein sequences
  • Pathway Visualization: Explore canonical signaling and metabolic pathways or build, based on curated relationships, custom networks, and overlay known disease and drug associations
  • Network analysis: Identify networks enriched with members of your gene set

(from geneXplain)

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