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 occurrences for over/under-representation compared to a reference.
4. Generate multiple visualizations for these analyses.
5. Generate input for Cytoscape, IGB, and Primer3