PAINT: Promoter Analysis and Interaction Network Toolset (V 4.0-pre)

Highly parallel gene expression analysis has led to analysis of gene regulation, in particular co-regulation, at a system level. PAINT was developed to provide the biologist a computational tool to integrate functional genomics data, for example from microarray-based gene expression analysis, with genomic sequence data to carry out transcriptional regulatory network analysis, TRNA. TRNA combines bioinformatics, used to identify and analyze gene regulatory regions, and statistical significance testing, used to rank the likelihood of the involvement of individual transcription factors, with visualization tools to identify transcription factors likely to play a role in the biology under study. In addition this tool can output results in several different formats such as Cytoscape format, IGB format, for use with modeling and simulation. As well as Primer3 output primers for hypothesized feasnet.
Given a list of genes, probeIds, mir based Ids, PAINT can:
  1. Fetch potential promoter sequences for the genes in the list.
  2. Find Transcription Factor (TF) binding sites on the sequences.
  3. Analyze the TF-binding site occurences for over/under-representation compared to a reference.
  4. Generate multiple visualizations for these analyses.
  5. Generate input for Cytoscape, IGB, and Primer3
Using PAINT    [ Documentation ]     [ Example ]

PAINT Version 4.0-pre: What's new (PAINT 3.9 Continues to be available at:


PAINT uses TRANSFAC Professional or TRANSFAC Public databases to predict known TF binding sites.
TRANSFAC Public: Register at to get a free account.
TRANSFAC Professional: Contact to purchase a license.

Citing PAINT

1. Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. OMICS. 2003 Fall;7(3):235-52.
Link to the publication

2. Gonye, G.E., Chakravarthula, P., Schwaber, J.S., Vadigepalli, R.: From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT (Chapter 4) in Methods in Molecular Biology: Gene Function Analysis, edited by Michael Ochs. Totowa: Humana Press, 408:49-68, 2007.
Link to Book info at Publisher's website

Licensing and Contact Information