ChIP-Seq - Identify and classify target genes

Created: 2013-11-13 15:35:48      Last updated: 2015-04-17 13:52:15

This workflow identifies and classifies target genes using positional information of peaks found by ChiP-Seq approach. As input, the peak regions in BED format, can be submitted. Actually, any dataset in BED format can be submitted as input track for this workflow.

First, the track file is converted into a gene set using Track to gene set analysis. The Ensembl gene list is then annotated with additional information, gene descriptions and chromosomal location.

The annotated Ensembl genes are submitted to Functional  classification using the following ontologies: GO biological processes, GO cellular components, GO molecular function, TF classification, Reactome and HumanCyc pathways.

In parallel with the Functional  classification, the Ensembl gene list is converted to a list of Entrez genes, which are used in the next analysis Cluster by shortest path to find clusters at 2 steps in both directions, upstream and downstream, from the input genes.  The clustering is performed using GeneWays network.

As output, a new folder is formed, which contains Functional  classification results, a list of annotated Ensemble genes and a diagram of clustered GeneWays genes.

What is the geneXplain type?

The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (, which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual workflows (geneXplain type), or Bricks, are unified under a standardized interface.
To run the workflows you just need to register for a free account here:

You get a password from BioStore to login the platform. It is open for everyone.

After clicking the workflow link (bottom) you can immediately enter the platform and execute the workflow via simple drag and drop of uploaded data files in your project.

Workflow_ChIP-Seq - Identify and classify target genes

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