ModuleDigger: An itemset mining framework for the detection of cis-regulatory modules

BMC Bioinformatics

Volumn 10, Issue SUPPL. 1, 2009, Pages

  Sun, Hong ^a   De Bie, Tijl ^b   Storms, Valerie ^c   Fu, Qiang ^c   Dhollander, Thomas ^a   Lemmens, Karen ^a   Verstuyf, Annemieke ^c   De Moor, Bart ^a   Marchal, Kathleen ^c  

^a Katholieke Universiteit Leuven   (Belgium)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

CIS-REGULATORY MODULES; CO-REGULATED GENES; COMBINATORIAL PROBLEM; DETECTION TOOLS; OPTIMIZATION METHOD; SCORING SCHEMES; TRANSCRIPTION FACTOR BINDING SITES; TRANSCRIPTIONAL RESPONSE;

BENCHMARKING; TRANSCRIPTION FACTORS; GENES;

GENES; BIOINFORMATICS;

EUKARYOTA;

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETIC DATABASE; METABOLISM; REGULATORY SEQUENCE;

ALGORITHMS; BINDING SITES; DATABASES, GENETIC; MODELS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 60849130409     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S30     Document Type: Conference Paper

References (19)

1. Davidson E Genomic Regulatory Systems: Development and Evolution San Diego, CA: Academic Press 2001.
2. Zhou Q Wong WH CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling Proc Natl Acad Sci U S A 2004, 101:12114-12119 514443 15297614 10.1073/pnas.0402858101
3. Aerts S Van Loo P Moreau Y De Moor B A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes Bioinformatics 2004, 20:1974-1976 10.1093/bioinformatics/bth179 15044242
4. Sharan R Ovcharenko I Ben Hur A Karp RM CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments Bioinformatics 2003, 19(Suppl 1):i283-i291 10.1093/bioinformatics/ btg1039 12855471
5. Gupta M Liu JS De novo cis-regulatory module elicitation for eukaryotic genomes Proc Natl Acad Sci U S A 2005, 102:7079-7084 1129096 15883375 10.1073/pnas.0408743102
6. Frith MC Fu Y Yu L Chen JF Hansen U Weng Z Detection of functional DNA motifs via statistical over-representation Nucleic Acids Res 2004, 32:1372-1381 390287 14988425 10.1093/nar/gkh299
7. Van Loo P Aerts S Thienpont B De Moor B Moreau Y Marynen P ModuleMiner - improved computational detection of cis-regulatory modules: Are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol 2008, 9:R66 10.1186/gb-2008-9-4-r66 18394174
8. Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A et al: TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes Nucleic Acids Res 2006, 34:D108-D110 1347505 16381825 10.1093/ nar/gkj143
9. Hertzberg L Zuk O Getz G Domany E Finding motifs in promoter regions J Comput Biol 2005, 12:314-330 10.1089/cmb.2005.12.314 15857245
10. Zaki MJ Hsiao C CHARM: An efficient algorithm for Closed Itemset Mining Proceedings of the Second SIAM International Conference on Data Mining (SDM '02) Grossman R, Han J, Kumar V, Mannila H, Motwani R 2002:457-473
11. Boyer LA Lee TI Cole MF Johnstone SE Levine SS Zucker JP et al. Core transcriptional regulatory circuitry in human embryonic stem cells Cell 2005, 122:947-956 10.1016/j.cell.2005.08.020 16153702
12. Wasserman WW Sandelin A Applied bioinformatics for the identification of regulatory elements Nat Rev Genet 2004, 5:276-287 10.1038/nrg1315 15131651
13. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci U S A 2001, 98:5116-5121 33173 11309499 10.1073/pnas.091062498
14. Kent WJ Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM The human genome browser at UCSC Genome Res 2002, 12:996-1006 186604 12045153
15. Aerts S Van Loo P Thijs G Mayer H de Martin R Moreau Y TOUCAN 2: The all-inclusive open source workbench for regulatory sequence analysis Nucleic Acids Res 2005 33(Web server issue):W393-W396 1160115 15980497 10.1093/nar/gki354
16. Coessens B Thijs G Aerts S Marchal K De Smet F Engelen K INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis Nucleic Acids Res 2003, 31:3468-3470 10.1093/nar/gkg615 12824346 169021
17. Thijs G Marchal K Lescot M Rombauts S De Moor B Rouze P A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes J Comput Biol 2002, 9:447-464 10.1089/ 10665270252935566 12015892
18. Gallo A De Bie T Cristianini N MINI: Mining Informative Non-redundant Itemsets Proceedings of the 11th conference on Principles and Practice of Knowledge Discovery in Databases (PKDD07), Warsaw, September 2007
19. ModuleDigger: An itemset mining framework for the detection of cis-regulatory modules 2008 http://homes.esat.kuleuven.be/~hsun/ ModuleDigger/Index.html