PAINT: Promoter Analysis and Interaction Network Toolset (V 3.5)
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 for use
with modeling and simulation tools.
Given a list of genes, PAINT can:
Fetch potential promoter sequences for the genes in the list.
Find Transcription Factor (TF) binding sites on the sequences.
Analyze the TF-binding site occurences for over/under-representation compared to a reference.
Generate multiple visualizations for these analyses.
