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Updated: Feb 22, 2026

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.

Divya Tej Sowpati¹, Surabhi Srivastava², Jyotsna Dhawan¹

¹CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.

BMC Bioinformatics

|September 21, 2017

Summary

This summary is machine-generated.

Bench biologists can now analyze multi-gene epigenetic patterns with C-State, a fast, interactive web app. This tool simplifies chromatin-state analysis and visualization, requiring no programming knowledge.

Keywords:

ChIP-seq Chromatin state Epigenetic patterns Genome browser JavaScript RNA-seq Visualization Web app

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Comparative epigenomic analysis across multiple genes is a significant bottleneck for researchers using next-generation sequencing (NGS) data.
Existing standardized peak analysis algorithms do not fully address the challenge of identifying and visualizing novel epigenetic patterns across gene subsets.

Purpose of the Study:

To develop a user-friendly and efficient tool for comparative epigenomic analysis.
To enable bench biologists to query and visualize chromatin landscapes across multiple genes and cell types without requiring programming expertise.

Main Methods:

Development of a fast and interactive web application named C-State (Chromatin-State).
Implementation of a JavaScript-based graphical user interface (GUI) for local execution in web browsers.
Elimination of requirements for extensive data transfer, pre-processing, or prior programming knowledge.

Main Results:

C-State provides a fast and interactive platform for querying and plotting chromatin landscapes.
The application enables visualization of epigenetic patterns across multiple loci and cell types.
C-State runs locally, streamlining the analysis workflow for bench biologists.

Conclusions:

C-State offers a unique capability for extracting and analyzing multi-gene epigenetic information.
The tool facilitates powerful GUI-based pattern searching and visualization of epigenetic data.
A case study demonstrates C-State's utility in identifying epigenetic trends correlated with gene expression profiles.