Related paper: Zhou, Q. and Wong, W.H. (2004). CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proceedings of the National Academy of Sciences USA, 101: 12114-12119.
Datasets used in the CisModule paper.
1. Simulated datasets: See readme.txt
for parameter settings and notes. simulation1.zip; simulation2.zip;
2. Drosophila dataset and related reference website;
3. Muscle specific genes dataset and related reference website;
Recent updates about CisModule (12/5/2005):
1. (12/5/05) We have implemented the "collapsed" version of CisModule, in which the parameters (such as PWMs) are integrated out in an approximate manner in the interative sampling. From our tests and experiences, this usually improves the convergence and efficiency of CisModule. Thus we have set this new implementation as the default setting. If you wish to use the original scheme (i.e. the data augmentation framework), you need to add "-P" in your command line.
2. (4/15/05) We added one more user-input parameter (-c) which specifies the threshold for output motif sites. This parameter should be between 0 and 1 since it represents a probability threshold. The default value for -c is 0.5. If CisModule predicts more sites than your expectation, you may try to increase this parameter.
Download CisModule.
Please download the readme file for CisModuleU and CisModuleOS with a test data set.
1. CisModuleU (Linux executable).
Put this tar file in a Linux directory and use "tar xvf CisModuleU.tar" to unpack
the file. Then type "./CisModuleU" for user manual.
The latest update was performed on Dec. 5, 2005.
2. CisModuleOS (OS executable).
Put this tar file in an OS directory and use "tar xvf CisModuleOS.tar" to unpack
the file. Then type "./CisModuleOS" for user manual.
The latest update was performed on Dec. 5, 2005.
3. CisModuleW (Windows executable).
The latest update was performed on Dec. 5, 2005.
If you have difficulties in running the above executable programs in your system, please try to compile CisModule from the C++ source code via "g++ *.cpp -lm -o CisModule -O3".
Please run repeat masker before using CisModule.
Link to a related program that detects cis-regulatory modules with given motif patterns: CisModScan.
Link to a module discovery program in multiple species:
MultiModule.