ModuleMiner - Computational Detection of cis-regulatory modules

ModuleMiner

Manuscript

Van Loo P., Aerts S., Thienpont B., De Moor B., Moreau Y. & Marynen P. (2008). ModuleMiner: improved computational detection of cis-regulatory modules. Different modes of gene regulation in embryonic development and adult tissues? Genome Biology, 9:R66.

Supplementary data: ModuleMiner results

Run ModuleMiner

ModuleMiner can be executed through this webpage. It requires selection of a whole genome database of transcription factor binding sites and a list of genes. Your run will be queued and results will be emailed when your run is complete (this can take up to one week).

Database:
1. Sequences: human-mouse conserved non-coding sequences, 10 kb 5' of TSS, based on Ensembl 36 and selected using LAGAN (75 % identity over 100 bp). Transcription factor binding site predictions: MotifScanner (prior = 0.2).
2. Sequences: human-mouse conserved non-coding sequences, 10 kb 5' of TSS, based on Ensembl 36 and selected using LAGAN (75 % identity over 100 bp). Transcription factor binding site predictions: MotifScanner (prior = 0.2) - only binding sites were retained for transcription factors also showing binding sites on the orthologous mouse region.
3. Sequences: human-mouse conserved non-coding sequences, 10 kb 5' of TSS, based on Ensembl 36 and selected using LAGAN (75 % identity over 100 bp) - to correct for possible differences in TSS, the mouse sequence was extended by 100kb in both directions for this alignment. Transcription factor binding site predictions: MotifScanner (prior = 0.2) - only binding sites were retained for transcription factors also showing binding sites on the orthologous mouse region.
Select a database:

List of genes (Ensembl gene IDs):
This can be either a comma separated list or a list separated by enters.
Example: "ENSG00000035403, ENSG00000100345, ENSG00000107796, ENSG00000108405, ENSG00000130176, ENSG00000133026, ENSG00000149591, ENSG00000154553, ENSG00000163017, ENSG00000163431, ENSG00000175084, ENSG00000183963"
Ensembl IDs for a set of genes can be obtained from Ensembl.
Enter your list of Ensembl IDs:

Email address where results should be mailed:

Note: one ModuleMiner run takes approximately one day. Runs started trough this webpage are queued. There is one exception: if a run with exactly the same parameters as previously is executed, the previous result is returned.

Contact

peter.vanloo<at>med.kuleuven.be