Identification of temporal association rules from time-series microarray data sets

BMC Bioinformatics

Volumn 10, Issue SUPPL. 3, 2009, Pages

  Nam, Hojung ^a   Lee, Ki Young ^b   Lee, Doheon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION RULE MININGS (ARM); DYNAMIC BAYESIAN NETWORKS; GENE EXPRESSION DATA; MICROARRAY GENE EXPRESSION DATA; REGULATION MECHANISMS; SACCHAROMYCES CEREVISIAE CELLS; TEMPORAL ASSOCIATION RULE; TEMPORAL ASSOCIATION RULE MININGS;

ASSOCIATION RULES; BAYESIAN NETWORKS; MICROARRAYS; TIME DELAY; YEAST;

GENE EXPRESSION;

BAYES THEOREM; BIOINFORMATICS; CELL CYCLE; CONFERENCE PAPER; DATA MINING; FUNGAL CELL; GENE EXPRESSION; GENE IDENTIFICATION; GENE REPRESSION; GENETIC DATABASE; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; SACCHAROMYCES CEREVISIAE; TIME SERIES ANALYSIS; ARTICLE; BIOLOGY; COMPARATIVE STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY;

SACCHAROMYCES CEREVISIAE;

BAYES THEOREM; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE;

EID: 63149102006     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S3-S6     Document Type: Conference Paper

References (37)

1. Kim DW Lee KH Lee D Detecting clusters of different geometrical shapes in microarray gene expression data Bioinformatics 2005, 21(9):1927-1934. 10.1093/bioinformatics/bti251 15647300
2. Ji L Tan KL Mining gene expression data for positive and negative co-regulated gene clusters Bioinformatics 2004, 20(16):2711-2718. 10.1093/bioinformatics/bth312 15145808
3. Ji L Tan KL Identifying time-lagged gene clusters using gene expression data Bioinformatics 2005, 21(4):509-516. 10.1093/bioinformatics/bti026 15374868
4. Tamada Y Kim S Bannai H Imoto S Tashiro K Kuhara S Miyano S Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection Bioinformatics 2003, 19(Suppl 2):iI227-236. 14534194
5. Liang S Fuhrman S Somogyi R Reveal, a general reverse engineering algorithm for inference of genetic network architectures Pac Symp Biocomput 1998, 18-29. 9697168
6. Akutsu T Miyano S Kuhara S Algorithms for inferring qualitative models of biological networks Pac Symp Biocomput 2000, 293-304. 10902178
7. Friedman N Learning bayesian network structure from massive datasets: the 'sparse candidate' algorithm Proc of Fifteenth Conference on Uncertainty in Artificial Intelligence 1999.
8. 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(2):166-176. 10.1038/ng1165 12740579
9. Lee PH Lee D Modularized learning of genetic interaction networks from biological annotations and mRNA expression data Bioinformatics 2005, 21(11):2739-2747. 10.1093/bioinformatics/bti406 15797909
10. Creighton C Hanash S Mining gene expression databases for association rules Bioinformatics 2003, 19(1):79-86. 10.1093/bioinformatics/19.1.79 12499296
11. Georgii E Richter L Ruckert U Kramer S Analyzing microarray data using quantitative association rules Bioinformatics 2005, 21(Suppl 2):iI123-129. 10.1093/bioinformatics/bti1121 16204090
12. Carmona-Saez P Chagoyen M Rodriguez A Trelles O Carazo JM Pascual-Montano A Integrated analysis of gene expression by Association Rules Discovery BMC Bioinformatics 2006, 7:54. 1386712 16464256 10.1186/ 1471-2105-7-54
13. Becquet C Blachon S Jeudy B Boulicaut JF Gandrillon O Strong-association-rule mining for large-scale gene-expression data analysis: A case study on human SAGE data Genome Biol 2002, 3:12. RESEARCH0067 151169 12537556 10.1186/gb-2002-3-12-research0067
14. Morgan XC Ni S Miranker DP Iyer VR Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining BMC Bioinformatics 2007, 8(1):445. 2211755 18005433 10.1186/1471-2105-8-445
15. Perrin BE Ralaivola L Mazurie A Bottani S Mallet J d'Alche-Buc F Gene networks inference using dynamic Bayesian networks Bioinformatics 2003, 19(Suppl 2):iI138-148. 14534183
16. Zou M Conzen SD A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data Bioinformatics 2005, 21(1):71-79. 10.1093/bioinformatics/bth463 15308537
17. Kikuchi S Tominaga D Arita M Takahashi K Tomita M Dynamic modeling of genetic networks using genetic algorithm and S-system Bioinformatics 2003, 19(5):643-650. 10.1093/bioinformatics/btg027 12651723
18. Husmeier D Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks Bioinformatics 2003, 19(17):2271-2282. 10.1093/bioinformatics/btg313 14630656
19. Qian J Dolled-Filhart M Lin J Yu H Gerstein M Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions J Mol Biol 2001, 314(5):1053-1066. 10.1006/jmbi.2000.5219 11743722
20. Filkov V Skiena S Zhi J Analysis techniques for microarray time-series data J Comput Biol 2002, 9(2):317-330. 10.1089/10665270252935485 12015884
21. Kwon AT Hoos HH Ng R Inference of transcriptional regulation relationships from gene expression data Bioinformatics 2003, 19(8):905-912. 10.1093/bioinformatics/btg106 12761051
22. Kato M Hata N Banerjee N Futcher B Zhang MQ Identifying combinatorial regulation of transcription factors and binding motifs Genome Biol 2004, 5(8):R56. 507881 15287978 10.1186/gb-2004-5-8-r56
23. Wang W Cherry JM Nochomovitz Y Jolly E Botstein D Li H Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation Proc Natl Acad Sci USA 2005, 102(6):1998-2003. 548531 15684073 10.1073/pnas.0405537102
24. Ning H Yuan H Chen S Temporal Association Rules in Mining Method Multi-Symposiums on Computer and Computational Sciences 2006.
25. Li Y Ning P Wang XS Jajodia S Discovering Calendar-based Temporal Association Rules Proc of the 8th Int'l Symposium on Temporal Representation and Reasoning 2001.
26. Doddi S Marathe A Ravi SS Torney DC Discovery of association rules in medical data Med Inform Internet Med 2001, 26(1):25-33. 10.1080/ 14639230010028786 11583406
27. Kanehisa M Goto S Hattori M Aoki-Kinoshita KF Itoh M Kawashima S Katayama T Araki M Hirakawa M From genomics to chemical genomics: New developments in KEGG Nucleic Acids Res 2006, 34: Database D354-357. 1347464 16381885 10.1093/nar/gkj102
28. Kanehisa M Goto S Kawashima S Nakaya A The KEGG databases at GenomeNet Nucleic Acids Res 2002, 30(1):42-46. 99091 11752249 10.1093/nar/30.1.42
29. Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9(12):3273-3297. 25624 9843569
30. Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes Science 2004, 306(5701):1555-1558. 10.1126/science.1099511 15567862
31. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25(1):25-29. 10.1038/75556 10802651
32. Krogan NJ Cagney G Yu H Zhong G Guo X Ignatchenko A Li J Pu S Datta N Tikuisis AP et al Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006, 440(7084):637-643. 10.1038/ nature04670 16554755
33. Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL Millar A Taylor P Bennett K Boutilier K et al Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415(6868):180-183. 10.1038/415180a 11805837
34. Fukuma M Hiraoka Y Sakurai H Fukasawa T Purification of yeast histones competent for nucleosome assembly in vitro Yeast 1994, 10(3):319-331. 10.1002/yea.320100305 8017102
35. Grant PA Eberharter A John S Cook RG Turner BM Workman JL Expanded lysine acetylation specificity of Gcn5 in native complexes J Biol Chem 1999, 274(9):5895-5900. 10.1074/jbc.274.9.5895 10026213
36. Gelbart ME Rechsteiner T Richmond TJ Tsukiyama T Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: Analyses using recombinant yeast histones and immobilized templates Mol Cell Biol 2001, 21(6):2098-2106. 86823 11238944 10.1128/MCB.21.6.2098-2106.2001
37. Gavin AC Aloy P Grandi P Krause R Boesche M Marzioch M Rau C Jensen LJ Bastuck S Dumpelfeld B et al Proteome survey reveals modularity of the yeast cell machinery Nature 2006, 440(7084):631-636. 10.1038/nature04532 16429126