This article is part of the supplement: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)
Research
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
-
* Corresponding author: Kathleen Marchal kathleen.marchal@biw.kuleuven.be
1 Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
2 Department of Engineering Mathematics, university of Bristol, Bristol BS8 1TR, UK
3 Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
4 Laboratory for experimental medicine and endocrinology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
BMC Bioinformatics 2009, 10(Suppl 1):S30 doi:10.1186/1471-2105-10-S1-S30
Published: 30 January 2009Additional files
Additional file 1:
Motif models from TRANSFAC. Additional file 1 is a text file that contains the motif matrices for OCT4, SOX2 and NANOG and 584 other regulators as obtained from TRANSFAC.
Format: TXT Size: 127KB Download file
Additional file 2:
The sets of 10, 20, 30, 40 regulators used for benchmarking ModuleDigger. Additional file 2 is a text file. Additional file 2 contains the regulator names that were selected in addition to the three regulators OCT4, SOX2 and NANOG but also the regulator names that were used for construction of the completely random sets. These data sets were used as input for ModuleDigger.
Format: TXT Size: 36KB Download file
Additional file 3:
The sets of 4 and 10 regulators used for comparing ModuleDigger with other CRM detection tools. Additional file 3 is a text file. Additional file 3 contains the regulator names that were selected in addition to the three regulators OCT4, SOX2 and NANOG. These data sets were used as input for ModuleDigger and other CRM module detection tools.
Format: TXT Size: 3KB Download file
Additional file 4:
List of 116 genes. Additional file 4 is a text file that contains the gene names of the 116 genes that were retrieved from the 353 genes originally listed as being cobound by OCT4, SOX2 and NANOG [11].
Format: TXT Size: 1KB Download file
Additional file 5:
The 5000 random genes. Additional file 5 is a text file and describes the 5000 randomly selected background genes that were used to calculate the coexpression specificity score. These additional files are also available on our supplementary website [19].
Format: TXT Size: 78KB Download file