Validating module network learning algorithms using simulated data

BMC Bioinformatics

Volumn 8, Issue SUPPL. 2, 2007, Pages

  Michoel, Tom ^a   Maere, Steven ^a   Bonnet, Eric ^a   Joshi, Anagha ^a   Saeys, Yvan ^a   Van den Bulcke, Tim ^b   Van Leemput, Koenraad ^c   Van Remortel, PieT ^c   Kuiper, Martin ^a   Marchal, Kathleen ^b   Van de Peer, Yves ^a  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING STRATEGY; CONDITIONAL ENTROPY; FUNCTIONAL VALIDATION; FURTHER DEVELOPMENT; GENE EXPRESSION DATA; HIER-ARCHICAL CLUSTERING; PROBABILISTIC GRAPHICAL MODELS; REGULATION PROJECTS;

ENTROPY; GENE EXPRESSION; LEARNING SYSTEMS; SOFTWARE PACKAGES;

LEARNING ALGORITHMS;

ALGORITHM; ARTICLE; BAYESIAN LEARNING; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; MACHINE LEARNING; VALIDATION PROCESS; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; EVALUATION; GENE EXPRESSION REGULATION; METABOLISM; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; VALIDATION STUDY;

PROTEOME;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; PATTERN RECOGNITION, AUTOMATED; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; SOFTWARE VALIDATION; SYSTEMS BIOLOGY;

EID: 34249845809     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S2-S5     Document Type: Article

References (36)

1. Ideker T Galitski T Hood L A new approach to decoding life: Systems biology Annu Rev Genomics Hum Genet 2001, 2:343-372 10.1146/ annurev.genom.2.1.343 11701654
2. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29 10.1038/75556 10802651
3. Friedman N Linial M Nachman I Pe'er D Using Bayesian networks to analyze expression data J Comput Biol 2000, 7:601-620 10.1089/106652700750050961 11108481
4. Pe'er D Regev A Elidan G Friedman N Inferring subnetworks from perturbed expression profiles Bioinformatics 2001, 17(Suppl 1):S215-S224 11473012
5. Bar-Joseph Z Gerber GK Lee TI Rinaldi NJ Yoo JY Robert F Gordon DB Fraenkel E Jaakkola TS Young RA Gifford DK Computational discovery of gene modules and regulatory networks Nat Biotechnol 2003, 21:1337-1342 10.1038/nbt890 14555958
6. Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 2003, 34:166-167 12740579
7. Beer MA Tavazoie S Predicting gene expression from sequence Cell 2004, 117:185-198 10.1016/S0092-8674(04)00304-6 15084257
8. Friedman N Inferring cellular networks using probabilistic graphical models Science 2004, 303:799-805 10.1126/science.1094068 14764868
9. Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J Jennings EG Zeitlinger J Pokholok DK Kellis M Rolfe PA Takusagawa KT Lander ES Gifford DK Fraenkel E Young RA Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431:99-104 10.1038/nature02800 15343339
10. Luscombe NM Madan Babu M Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431:308-312 10.1038/nature02782 15372033
11. Xu X Wang L Ding D Learning module networks from genome-wide location and expression data FEBS Lett 2004, 578:297-304 10.1016/ j.febslet.2004.11.019 15589836
12. Battle A Segal E Koller D Probabilistic discovery of overlapping cellular processes and their regulation J Comput Biol 2005, 12:909-927 10.1089/cmb.2005.12.909 16201912
13. Basso K Margolin AA Stolovitzky G Klein U Dalla-Favera R Califano A Reverse engineering of regulatory networks in human B cells Nat Genet 2005, 37:382-390 10.1038/ng1532 15778709
14. Garten Y Kaplan S Pilpel Y Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data Nucleic Acids Res 2005, 33:605-615 548334 15684410 10.1093/nar/gki166
15. Petti AA Church GM A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae Genome Res 2005, 15:1298-1306 1199545 16109970 10.1101/gr.3847105
16. Lemmens K Dhollander T De Bie T Monsieurs P Engelen K Smets B Winderickx J De Moor B Marchal K Inferring transcriptional modules from ChIP-chip, motif and microarray data Genome Biol 2006, 7:R37 1779513 16677396 10.1186/gb-2006-7-5-r37
17. Van den Bulcke T Lemmens K Van de Peer Y Marchal K Inferring transcriptional networks by mining 'omics' data Current Bioinformatics 2006, 1:301-313
18. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999, 402:C47-C52 10.1038/35011540 10591225
19. Segal E Friedman N Kaminski N Regev A Koller D From signatures to models: Understanding cancer using microarrays Nat Genet 2005, 37:S38-S45 10.1038/ng1561 15920529
20. Van den Bulcke T Van Leemput K Naudts B van Remortel P Ma H Verschoren A De Moor B Marchal K SynTReN: A generator of synthetic gene expression data for design and analysis of structure learning algorithms BMC Bioinformatics 2006, 7:43 1373604 16438721 10.1186/1471-2105-7-43
21. Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11:4241-4257 15070 11102521
22. Butte AJ Kohane IS Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements Pac Symp Biocomput 2000, 5:418-429
23. Butte A Tamayo P Slonim D Golub T Kohane I Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks PNAS 2000, 97:12182-12186 17315 11027309 10.1073/pnas.220392197
24. Pe'er D Regev A A T Minreg: Inferring an active regulator set Bioinformatics 2002, 18(Suppl 1):S258-S267 12169555
25. Sinkkonen J Kaski S Clustering based on conditional distributions in an auxiliary space Neural Comput 2002, 14:217-239 10.1162/ 089976602753284509 11747539
26. Kasturi J Acharya R Ramanathan M An information theoretic approach for analyzing temporal patterns of gene expression Bioinformatics 2003, 19:449-458 10.1093/bioinformatics/btg020 12611799
27. Genomica http://genomica.weizmann.ac.il
28. Saccharomyces Genome Database http://www.yeastgenome.org/
29. Ma HW Kumar B Ditges U Gunzer F Buer J Zeng AP An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs Nucleic Acids Res 2004, 32:6643-6649 545451 15604458 10.1093/nar/gkh1009
30. Segal E Pe'er D Regev A Koller D Friedman N Learning module networks Journal of Machine Learning Research 2005, 6:557-588
31. Heller KA Ghahramani Z Bayesian hierarchical clustering Proceedings of the twenty-second International Conference on Machine Learning 2005
32. Shannon CE A mathematical theory of communication The Bell System Technical Journal 1948, 27:379-423 http://cm.bell-labs.com/cm/ms/what/ shannonday/paper.html 623-656
33. de Hoon MJL Imoto S Nolan J Miyano S Open source clustering software Bioinformatics 2004, 20:1453-1454 10.1093/bioinformatics/bth078 14871861
34. Maere S Heymans K Kuiper M BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks Bioinformatics 2005, 21:3448-3449 10.1093/bioinformatics/bti551 15972284
35. SynTReN http://homes.esat.kuleuven.be/~kmarchal/SynTReN
36. LeMoNe http://bioinformatics.psb.ugent.be/LeMoNe/download.htm