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BIOBASE: Overview

Main Applications

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

Genome Trax: functional annotation tool for sequencing data

  • Genome Trax maps manually curated Biobase contents, including regulatory sites from TRANSFAC, disease mutations from HGMD, biomarkers from PROTEOME, and 3rd party genomic variation features onto user NGS data. The mapping results can be directly outputted to major genome browsers.

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. 

ExPlain: unique data analysis workflow that combines functional classification and transcription regulation analyses

  • Explain investigates how transcription factors act together to affect gene expression.  With ExPlain's pathway data, users can gain insight into the key upstream signaling regulators influencing the activity of these transcription factors and identify key therapeutic targets or biomarkers.

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

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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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