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Chromatin Immunoprecipitation- ChIP

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Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Published on: April 19, 2013

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

Taiyun Kim¹, Hani Jieun Kim², Andrew J Oldfield³

¹Computational 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.

|March 31, 2023

Summary

This study introduces PAD2, a web tool for analyzing transcription factor (TF) genomic colocalization. PAD2 helps researchers understand how TFs work together to control gene expression in mouse embryonic stem cells.

Keywords:

Bioinformatics Genomics Sequence Analysis Stem Cells Systems Biology

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Last Updated: Aug 4, 2025

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Understanding transcription factor (TF) interactions is crucial for deciphering gene regulation.
Genomic colocalization analysis reveals cooperative binding of TFs.
Existing methods may lack user-friendly interfaces for exploring TF colocalization data.

Purpose of the Study:

To introduce PAD2, an interactive web application for investigating TF and chromatin-regulating protein colocalization.
To provide a protocol for utilizing PAD2 to analyze TF binding patterns in functional genomic regions.
To facilitate the identification of cooperative TF binding events in mouse embryonic stem cells.

Main Methods:

Development of PAD2, a web-based application for genomic data visualization and analysis.
Protocol detailing database access, genomic region selection, and data submission within PAD2.
Implementation of heatmap and ranked correlation plots for protein colocalization analysis.

Main Results:

PAD2 enables interactive exploration of TF and protein colocalization across diverse genomic regions.
The protocol guides users through data retrieval and analysis of colocalization patterns.
Visualizations like heatmaps effectively represent protein association strengths.

Conclusions:

PAD2 serves as a valuable resource for researchers studying TF cooperative binding.
The protocol simplifies the process of analyzing TF colocalization in mouse embryonic stem cells.
This tool aids in understanding the mechanisms of gene expression control through TF interactions.