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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

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Published on: April 5, 2018

Meta-analysis of Genome-Wide Chromatin Data.

Julia Engelhorn¹, Franziska Turck²

¹Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Köln, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|October 23, 2016

Summary

This study presents a meta-analysis workflow to interpret genome-wide target gene lists. It integrates transcriptional data and functional enrichment analysis using Gene Ontology (GO) to reveal hidden biological functions.

Keywords:

AtGenExpress Functional enrichment analysis Gene Ontology Hierarchical clustering K-means clustering Meta-analysis

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Genome-wide studies identify numerous potential target genes.
Annotation databases aid in genomic dataset characterization.
Meta-analysis enables multi-database comparisons for deeper insights.

Purpose of the Study:

To describe a workflow for transcriptional and functional analysis of genome-wide target genes.
To demonstrate the utility of meta-analysis in uncovering hidden functions within genomic datasets.

Main Methods:

Utilizing transcription data sources and clustering tools for gene expression pattern analysis.
Employing the Gene Ontology (GO) vocabulary for functional enrichment analysis.
Applying meta-analysis to genomic targets of histone modification H3K27me3 as a case study.

Main Results:

The workflow integrates gene expression patterns with functional annotations.
Gene Ontology analysis identifies over- or underrepresented functions among target genes.
Case study demonstrates meta-analysis revealing previously hidden functions.

Conclusions:

A robust workflow for analyzing genome-wide target genes is presented.
Meta-analysis, combined with GO, enhances the functional interpretation of genomic data.
This approach is effective in uncovering biological functions obscured in large datasets.