ExPlain Analysis System
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BIOBASE ExPlain™ is a unique data analysis system that combines promoter and pathway analysis tools. Using the power of TRANSFAC®’s transcription factor binding site derived positional weight matrices, ExPlain™ enables you to identify transcription factors affecting gene expression in your microarray and RNA-Seq experiments, as well as predict how they, in combination, can induce observed gene expression patterns. With PROTEOME™’s pathway data, you can take your analysis further and gain insight into the key upstream signaling regulators influencing the activity of these transcription factors.



  • Perform high throughput prediction of transcription factor binding sites
  • Model how transcription factors act together to affect gene expression patterns observed in microarray and RNA-Seq experiments
  • Understand the cause, not just the effect, of differential expression in response to drug treatment, disease state, environmental conditions, and more
  • Identify potential therapeutic targets or biomarkers acting upstream of your differentially expressed gene set

Key Features

  • Advanced data management options for processing and filtering your microarray, ChIP-Seq and RNA-Seq data
  • Specialized algorithms for optimized transcription factor binding site prediction
  • Positional weight matrix algorithms for superior accuracy
  • Combined positional weight matrix and pattern matching algorithms for superior sensitivity
  • Genetic algorithms for generating complex promoter models
  • Discovery algorithms for identifying novel DNA motifs
  • Specialized algorithms and tools for advanced network and pathway analysis
  • Fully interlinked with TRANSFAC® and PROTEOME™ reports

Access Options

An online subscription provides access to the ExPlain 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.

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


Support Documents


Release 2012.4 – Available on-demand
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Video Tutorials

Data Input Types
Upload and analyze various data types.
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MATCH to Keynode Analysis
Promoter analysis allows you to find putative transcription factor binding sites in the promoters of a gene set or user-loaded sequences.
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Functional Analysis Module
Allows you to investigate the biological properties of any gene list.
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Archived Webinars

Upstream Analysis of Gene Expression Data
Analysis of TAL1 ChIP-seq Intervals

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