PROTEOME: Functional Analysis
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BIOBASE PROTEOME is a knowledgebase containing data on genes and miRNAs, the diseases they are associated with, the drugs they are targeted by, and the pathways and networks they act within.  Based on its extensive compilation of published functional attributes, the powerful ontology search query system allows scientists to quickly find answers to questions relevant to their research without reading through long lists of publications.  Specialized tools for gene and miRNA set analysis make it easy to identify shared functional characteristics and enriched interaction networks within lists of experimentally identified genes and miRNAs.  For complimentary gene regulation analysis options combine it with BIOBASE TRANSFAC®.




  • Quickly access detailed reports for individual genes, miRNAs, diseases, and drugs without tedious and time consuming literature searches
  • Uncover biologically relevant connections between seemingly disparate genes, diseases, and drugs
  • Map functional attributes to uploaded gene or miRNA sets, filtering by the most important and relevant criteria
  • Identify and rank potential therapeutic targets based on known functional characteristics
  • Explore canonical pathways and build custom protein networks, overlaying known disease and drug associations
  • Assign predictive functions to novel protein sequences

Key Features


  • Interlinked reports connecting genes, diseases, drugs, and pathways
  • 275,000+ gene reports for more than 20 species that include literature curated information about disease associations, pattern of expression, mutant phenotype, pathway assignments and more
  • View a sample report for Human DRD1 or Yeast MFALPHA1
  • 4,000+ mature miRNA reports which integrate miRBase structural data with literature curated information about disease associations, biological roles, pattern of expression and more
  • View a sample report for Human miR-125a-5p
  • 2,200+ disease reports that detail disease biomarker associations, including key information regarding causality, molecular alteration, and tissue specificity, as well as clinical information integrated from
  • View a sample report for Osteoporosis
  • 4,300+ drug reports that detail drug-protein interactions and the pathways that may be affected by therapeutic intervention, including information integrated from DrugBank and
  • Searchable access to over 980,000 functional assignments
  • A pathway visualization tool for building and exporting custom networks based on experimentally demonstrated protein-protein binding, signaling and transcriptional regulation interactions
  • A custom sequence annotation tool for assigning predictive functions to novel proteins

Access Options

An online subscription provides access to the PROTEOME web interface. Online subscriptions are available at the concurrent user, academic / non-profit lab, and institution-wide level. The concurrent user and academic / non-profit lab subscription levels require IP plus username/password authentication. IP only authentication is optionally available for the institution-wide subscription level.

API Download
An API download subscription allows for direct programmatic querying of PROTEOME locus, disease, drug and pathway reports in order to extract desired fields of information in XML format. An API download subscription also allows the programmatic analysis of gene sets for over-representation of biological process, molecular function and disease term assignments using either a simple Fisher test or LRpath (logistic regression) algorithm. In this way, PROTEOME data may be integrated into your own, or 3rd party, analysis pipelines and tools. However, redistribution of, or public access to/display of, the data is not allowed without prior written consent.

Relational Database Download
A relational database download subscription allows for local installation of the complete PROTEOME relational database, as well as access to the command line version of the BioKnowledge Transfer tool. A local installation allows you to query and extract all fields of PROTEOME data for integration into your own, or 3rd party, analysis pipelines and tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent. Relational database download subscriptions do not provide access to the PROTEOME web interface. MySQL platform is supported.

Click here for a table comparison of features available in online vs. download options.

Academic research user? Order now.
Commercial user/clinical, non-profit/academic service provider? Request a quote.


Support Documents

Research / Whitepapers

Scientific Publications

Video Tutorials

Pathfinder Tool
Using the Pathfinder visualization tool to review canonical pathways and to explore and build out protein and gene interaction networks.
>> Watch video

Network Analysis
Searching for protein and gene interaction networks enriched with members of an input list of genes link.
>> Watch video

Ontology Search
Powerful search and analysis tool that allows you to easily answer complex biological questions using the wealth of annotated information within the BKL.
>> Watch video

BKT Tool
The BioKnowledge Transfer (BKT) tool is used to assign predictive functions to uncharacterized proteins.
>> Watch video

Search and API
Find reports that pertain to genes or proteins, diseases, pathways and drugs.
>> Watch video


Release 2013.3 (September) – Watch video

Archived Webinars

API and Relational Database Access to Disease, Gene and Drug Content

>> View all webinars