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

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.

SUBMITTER: Kim T

PROVIDER: S-EPMC10090434 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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

Kim Taiyun T Kim Hani Jieun HJ Oldfield Andrew J AJ Yang Pengyi P

STAR protocols 20230329 2

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 r ...[more]

PMID: 37000617

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