Welcome to CisGenome!


(An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis)

Mirror Sites:

CisGenome @ Hopkins: http://www.biostat.jhsph.edu/~hji/cisgenome/

CisGenome @ Stanford: http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm

[The biogibbs server at Stanford went down. We are in the process of relocating the Stanford mirror site. We are sorry for the inconvenience. The jhsph sever will continue to provide all services during this period.]



03/30/2011: hmChIP is released! Using >2000 publicly available ChIP-seq and ChIP-chip profiles to help you understand your own biological system now becomes easier than ever. You can study context-dependency of cis-regulatory elements and find collaborating proteins  of your transcription factor of interest by taking advantage of public ChIP data from diverse cell types and for a variety of proteins. Check hmChIP database and web server here.

01/15/2011: CisGenome v2.0 is released! See Tutorial. This version contains a new ChIP-seq peak caller. The new peak caller is designed for experiments with both IP and control samples (i.e. two sample analysis). Features of the new algorithm include:

   (1) It is more robust than the old peak caller, and it requires much less memory. Most  of the memory issues in the old version will go away with the new algorithm.

   (2) It is able to handle biological/technical replicates.

   (3) One can now choose to use a dynamic read rate model which estimates background read sampling rate using a local window.


Copyright, 2007 – 11, The Johns Hopkins University.  All Rights reserved. 


Permission granted to download and use CisGenome for non-commercial research use only. No further distribution or copying for commercial use permitted without express written consent. Contact Hongkai Ji, Ph.D., Assistant Professor, Email: hji@jhsph.edu.

The three core components of CisGenome

What can I do with CisGenome?