ChromaSig is an unsupervised learning method to search for common patterns ("motifs") of histone modifications. Chromasig was proposed by Gary Hon et al.

Download ChromaSig1.0

Reference: ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome.


Chromia is supervised learning method that integrates epigenomic and genomic information to predict functional locis (e.g. promoters and enhancers) as well as TF binding sites. Chromia was proposed by Kyoung-Jae Won et al.

Chromia version for predicting functional locis
Chromia version for predicting TF binding sites


1. Prediction of regulatory elements in mammalian genomes using chromatin signatures.
2. Kyoung-Jae Won, Bing Ren and Wei Wang, Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol. 2010 Jan 22;11(1):R7.

  AnnoJ genome browser

Genome browser is a visualization tool that can be used to view data tracks from second generation sequencing platform. AnnoJ genome browser is a web 2.0 technology based program, which provides quick response and fast readering speed. Here we provide some programs and documents that can be used to set up and configure AnnoJ genome browser on your own computer.

Software packages required to set up envirnoment:
* Linux distributions: visit http://www.linux.org/ and linux distributions to get linux related information.
* GCC programming language: http://gcc.gnu.org/
* PERL programming language: http://www.perl.org/
* Apache http server: http://httpd.apache.org/
* PHP hypertext preprocessor: http://www.php.net/
* Oracle Berkeley DB: download linux version here

Download document and instructions to install those packages and set up environment for STAR genome browser.

If you want to quickly make your data tracks can be visualized in STAR genome browser, please download software packages here. You can learn details on how to do it from README.TXT
Download the data processing package

Some php files are required when you setup data visualization on your own computer. You can download them here and extract to your web document directory.
Download STAR browser website framework

  Cis-regulatory module finding

An integrated approach to identify cis-regulatory modules in human genome.

Data set

The ChIP data considering sonication
format: ENCODE chr_begin_end ratio p_value ratio2

creb.rst3,  e2f1.rst3,  max.rst3,  yy1.rst3

The output of GITTAR for 4 TFs

creb,  e2f1,  max,  yy1

The software

README,  IntHmm.tar.gz

Reference: Won K-J, Agarwal S, Shen L, Shoemaker R, Ren B, et al. (2009) An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome. PLoS ONE 4(5): e5501.


GBNet is designed to search for enriched sequence constraints such as a motif pair and positional preference of motif in a group of co-regulated genes.

Download GBNet

Reference: Li Shen, Jie Liu, Wei Wang, GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach, BMC Bioinformatics 2008, 9:395.


MODEM integrates sequence motif and gene expression or ChIP-binding data to identify TF binding sites. MODEM was developed by Wei Wang et al.

Download MODEM

Reference: Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation.


TransModis is a generalization of MODEM to consider sequence motif and multiple gene expression or ChIP-binding experiments to identify TF binding sites. Transmodis was proposed by Ron X.Yu and Jie Lie et al.

Download TransModis

Reference: Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16.