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Cis-regulatory Element Annotation System CEAS

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A software tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. CEAS provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone.

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1 user review

1 user review

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

I used it for ChIP-seq, to annotate Peaks. But I also used Homer tools and results were quite different.... for example in 5'-UTR (4.1% vs 2.4%). I guess it comes from the definition of what a region is, but I used a small file of 10 peaks and CEAS returned strange percentages... I think that CEAS splits a peak if it can fit in 2 regions, to check... I like the pie charts representation.

CEAS forum

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CEAS classification

CEAS specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
BED, WIG, sqlite3
Output format:
PDF, XLS, R
Programming languages:
Python
Stability:
Stable
Interface:
Command line interface
Input data:
ChIP regions, ChiP enrichment signal and gene annotation table file
Output data:
R script to generate the graphical results and gene-centered annotation in a tab-delimited txt file
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Maintained:
Yes

CEAS distribution

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CEAS forum

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No open topic.

CEAS classification

CEAS specifications

Interface:
Web user interface
Input format:
BED, GFF
Computer skills:
Basic
Source code URL:
http://ceas.cbi.pku.edu.cn/submit.htm
Restrictions to use:
None
Programming languages:
Python
Stability:
Stable
Maintained:
Yes

CEAS distribution

CEAS support

Maintainer

  • Hyunjin Shin <>
  • Hyunjin Shin <>

Credits

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Publications

Institution(s)

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, MA, USA

Link to literature

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