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

Taiyun Kim; Hani Jieun Kim; Andrew J Oldfield; Pengyi Yang

doi:10.1016/j.xpro.2023.102203

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

STAR Protoc. 2023 Mar 29;4(2):102203. doi: 10.1016/j.xpro.2023.102203. Online ahead of print.

Authors

Taiyun Kim¹, Hani Jieun Kim², Andrew J Oldfield³, Pengyi Yang⁴

Affiliations

¹ Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia. Electronic address: taiyun.kim@sydney.edu.au.
² Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
³ Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France.
⁴ Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia. Electronic address: pengyi.yang@sydney.edu.au.

Abstract

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. For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).¹.

Keywords: Bioinformatics; Genomics; Sequence Analysis; Stem Cells; Systems Biology.