Supplementary information

Dataset used in the study

One synthetic dataset

For the sequences we used data constructed by Xie et al. 2008, Genome Res. The data consists of 22 genomic sequences from mouse genome, each 1000 bp in length. In the first 20 sequences, transcription factors OCT4, SOX2 and FOXD3 are each inserted 3 times, in a region of at most 164 bp. The inserted nucleotides are sampled from the respective TRANSFAC PWMs. The last two sequences have no inserted transcription factors.

Inserted positions: Additional file 1
Co-regulated sequences, in FASTA format: Additional file 2
background sequences, in FASTA format: Additional file 3
516 non-redundant TRANSFAC PWMs used: Additional file 4
Ids and names of TRANSFAC PWMs used in the different samples: Additional file 5

Five ChIP-Seq dataset on mouse embryonic stem cell (ESC)

For the ChIP-Seq data we used from Chen et al. 2008, Cell. We download 5 binding peak files for five transcription factors KLF4, NANOG, OCT4, SOX2 and STAT3 from the GEO database with ID number GSE11431. Each of the data we use 100 genomic sequences, each 500 bp in length centering the top 100 binding peaks for transcription factors (TFs) KLF4, SOX2, OCT4, NANOG and STAT3 respectively.

5 set of sequences respectively centering top 100 binding peaks for TFs KLF4, SOX2, OCT4, NANOG and STAT3 in FASTA format: Additional file 6
Background sequences for stringent motif screening threshold strategy, in FASTA format: Additional file 7
Background sequences for lower motif screening threshold strategy and filtering, in Clover format: Additional file 8
516 non-redundant TRANSFAC PWMs and 1 KLF4 PWM used (Whitington et al. 2009, Nucl Acids Res by de novo motif detection on ChIP-chip data Jiang et al. 2008, Nature Cell Biology): Additional file 9

CPModule download and manual

CPModule

Guns, T., Sun, H., Marchal, K., Nijssen, S. (2010) Cis-regulatory module detection using constraint programming. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010) pages:363-368 (IEEE computer society).
Sun, H., Guns, T., Fierro, AC., Thorrez, L., De Moor, B., Nijssen, S., Marchal, K. (2011) Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. Submitted.

kathleen.marchal<at>biw.kuleuven.be

CPModule

CP4IM project website