PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data

Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TFs and chromatin-regulating proteins from mouse embryonic stem cells at various functional genomic regions. We describe steps for accessing and searching the PAD2 database and selecting and submitting genomic regions. We then detail protein colocalization analysis using heatmap and ranked correlation plot.

Automated summary

This article introduces a protocol for utilizing PAD2, an interactive web application, to investigate the colocalization of various transcription factors and chromatin-regulating proteins in mouse embryonic stem cells. The protocol includes steps for accessing and searching the PAD2 database, selecting and submitting genomic regions, and conducting protein colocalization analysis using heatmap and ranked correlation plot.