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BIOBASE: Overview

Main Applications

BIOBASE is a comprehensive suite of biomolecule knowledgebase and analysis tools.  

PROTEOME: manually curated knowledgebase for proteins

  • PROTEOME features disease, drug, biomarker and pathway information for proteins manually curated from PubMed abstracts and over 500 full-text publications.  Users can also perform statistical analysis to identify disease, pathways, or processes that are over-represented by a geneset of interest.    

TRANSFAC: largest Eukaryotic gene regulation database

  • TRANSFAC database covers the most comprehensive transcription regulation information, including experimentally validated transcription factor binding site, positional weight matrices (for transcription factor binding prediction), promoter sequences and features, miRNAs and their target sequences, and extensive structural and functional information on transcription factors and composite elements. 

HGMD (Human Gene Mutation Database):  comprehensive database for human inherited disease mutation

  • HGMD provides disease-related mutations information manually curated from peer review publications.  Search the database to determine the novelty of identified gene mutations, explore the genetic cause of a disease, or map mutations to a full genome. 


USC has licensed BIOBASE for the free use of USC faculty, students and staff.  The license consists of unlimited access to USC usersTo get your BIOBASE account:

  1. Carefully check out the BIOBASE user policy
  2. Fill out the BIOBASE registration form
  3. Activate your account following the link in the confirmation email sent out by BIOBASE (may take 1-2 days)
  4. Log in here to use BIOBASE

Need help?

Get started

BIOBASE consists of multiple products.  For each product, watch the introductory video to learn its basic features and general use instructions.  For detailed steps, watch the short videos. 


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