Discovering time-lagged rules from microarray data using gene profile classifiers

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Gallo, Cristian A ^a   Carballido, Jessica A ^a   Ponzoni, Ignacio ^a,b  

^a UNIVERSIDAD NACIONAL DEL SUR   (Argentina)

^b PLAPIQUI UNS CONICET   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE; GENE PROFILES; GENE REGULATORY NETWORKS; MICROARRAY DATA; MODEL FREE; MODEL-FREE ALGORITHMS; TIME-SERIES DATA;

BIOLOGY; COMBINATORIAL OPTIMIZATION; EVOLUTIONARY ALGORITHMS; INFERENCE ENGINES; MATHEMATICAL MODELS; TIME DELAY; TIME SERIES;

GENES;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 79955126373     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-123     Document Type: Article

References (57)

1. Zamani Z, Hajihosseini A, Masoudi-Nejad A. Computational Methodologies for Analyzing, Modeling and Controlling Gene Regulatory Networks. Biomedical Engineering and Computational Biology 2010, 2:47-62.
2. Karlebach G, Shamir R. Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 2008, 9:770-780. 10.1038/nrm2503, 18797474.
3. Alves R, Rodriguez-Baena DS, Aguilar-Ruiz JS. Gene association analysis: a survey of frequent pattern mining from gene expression data. Brief Bioinform 2010, 11:210-224. 10.1093/bib/bbp042, 19815645.
4. De Jong H. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. J Computational Biology 2002, 9:67-103.
5. Pridgeon C, Corne D. Genetic Network Reverse-Engineering and Network Size; Can We Identify Large GRNs?. Proc 2004 IEEE Symp Computational Intelligence in Bioinformatics and Computational Biology 2004, 32-36.
6. Li H, Xuan J, Wang Y, Zhan M. Inferring regulatory networks. Front Biosci 2008, 13:263-275. 10.2741/2677, 17981545.
7. Li X, Rao S, Jiang W, Li C, Xiao Y, Guo Z, Zhang Q, Wang L, Du L, Li J, Li L, Zhang T, Wang QK. Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling. BMC Bioinformatics 2006, 7:26. 10.1186/1471-2105-7-26, 1386718, 16420705.
8. Silvescu A, Honavar V. Temporal boolean network models of genetic networks and their inference from gene expression time series. Complex Systems 1997, 11:1-1+.
9. Yeang CH, Jaakkola T. Time series analysis of gene expression and location Data. Third IEEE Symposium on BioInformatics and BioEngineering (BIBE'03) Bethesda 2003, 305-312. Maryland: Institute of Electrical and Electronics Engineers, Inc.
10. Ponzoni I, Azuaje F, Augusto J, Glass D. Inferring Adaptive Regulation Thresholds and Association Rules from Gene Expression Data through Combinatorial Optimization Learning. IEEE/ACM Trans on Comp Biology and Bioinformatics 2007, 4(4):624-634.
11. Bulashevska S, Eils R. Inferring Genetic Regulatory Logic from Expression Data. Bioinformatics 2005, 21:2706-2713. 10.1093/bioinformatics/bti388, 15784747.
12. Soinov LA, Krestyaninova MA, Brazma A. Towards Reconstruction of Gene Networks from Expression Data by Supervised Learning. Genome Biology 2003, 4:R6. 10.1186/gb-2003-4-1-r6, 151290, 12540298.
13. van Someren EP, Wessels LF, Reinders MJ. Linear modeling of genetic networks from experimental data. Proc Int Conf Intell Syst Mol Biol 2000, 8:355-366.
14. Jiang D, Tang C, Zhang A. Cluster analysis for gene expression data: a Survey. IEEE Trans Knowl Data Eng 2004, 16:1370-86.
15. Madeira SC, Oliveira AL. Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans on Comp Biology and Bioinformatics 2004, 1:24-45.
16. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Andres K, Eisen B, Brown PO, Botstein D, Futcher B. Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell 1998, 9:3273-3297. 25624, 9843569.
17. Friedman FN, Linial M, Nachman I, Pe'er D. Using Bayesian Networks to Analyze Expression Data. J Computational Biology 2000, 7:601-620.
18. Zou M, Conzen SD. A New Dynamic Bayesian Network (DBN) Approach for Identifying Gene Regulatory Networks from Time Course Microarray Data. Bioinformatics 2005, 21:71-79. 10.1093/bioinformatics/bth463, 15308537.
19. Styczynski MP, Stephanopoulos G. Overview of Computational Methods for the Inference of Gene Regulatory Networks. Computers and Chemical Eng 2005, 29:519-534.
20. Agrawal R, Srikant R. Fast Algorithms for Mining Association Rules. Proc VLDB Conf 1994,
21. Baralis E, Bruno G, Ficarra E. Temporal association rules for gene regulatory networks. Proceedings of the 4th International IEEE Conference 2008, 2-7.
22. Nam H, Lee K, Lee D. Identification of temporal association rules from time series microarray data sets. BMC Bioinformatics 2009, 10(Suppl 3):S6. 10.1186/1471-2105-10-S3-S6, 2788357, 19958516.
23. Quinlan JR. C4.5: Programs for Machine Learning. 1992, Morgan Kaufmann.
24. Liang S, Fuhrman S, Somogyi R. REVEAL, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures. Proc Pacific Symp Biocomputing 1998, 3:18-29.
25. Akutsu T, Miyano S, Buhara S. Identification of Genetic Networks from a Small Number of Gene Expression Patterns under the Boolean Network Model. Proc Pacific Symp Biocomputing 1998, 4:17-28.
26. Mehra S, Hu WS, Karypis G. G: A Boolean Algorithm for Reconstructing the Structure of Regulatory Networks. Metabolic Eng 2004, 6:326-339.
27. Mitchel T. Machine Learning. 1997, WCB/McGraw-Hill.
28. Kohavi R. Wrappers for performance enhancement and oblivious decision graphs. PhD thesis 1995, Stanford University, Computer Science Department.
29. Lee I, Li Z, Marcotte EM. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS ONE 2007, 2(Suppl 10):e988. 1991590, 17912365.
30. Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 2002, 30:69-72. 10.1093/nar/30.1.69, 99086, 11752257.
31. Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28:21-28.
32. Stapley BJ, Benoit G. Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 2000, 529-540.
33. Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558. 10.1126/science.1099511, 15567862.
34. 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. Nature Genetics 2003, 34:166-176. 10.1038/ng1165, 12740579.
35. Yeang CH, Jaakkola T. Physical Network Models and Multi-Source Data Integration. Proc Seventh Ann Int'l Conf Research in Computational Molecular Biology 2003, 312-321.
36. Kuhne C, Linder P. A New Pair of B-Type Cyclins from Saccharomyces cerevisiae that Function Early in the Cell Cycle. European Molecular Biology Organization J 1993, 12:3437-3447.
37. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle. Molecular Biology of the Cell 2000, 11:369-391. 14780, 10637314.
38. Hwang LH, Lau LF, Smith DL, Mistrot CA, Hardwick KG, Hwang ES, Amon A, Murray AW. Budding Yeast CDC20: A Target of the Spindle Checkpoint. Science 1998, 279:1041-1044. 10.1126/science.279.5353.1041, 9461437.
39. Epstein CB, Cross FR. CLB5: A Novel B Cyclin from Budding Yeast with a Role in S Phase. Genes and Development 1992, 6:1695-1706. 10.1101/gad.6.9.1695, 1387626.
40. Levine K, Huang K, Cross FR. Saccharomyces cerevisiae G1 Cyclins Differ in Their Intrinsic Functional Specificities. Molecular and Cellular Biology 1996, 16:6794-6803. 231682, 8943334.
41. Althoefer H, Schleiffer A, Wassmann K, Nordheim A, Ammerer G. McmI Is Required to Coordinate G2-Specific Transcription in Saccharomyces cerevisiae. Molecular and Cellular Biology 1995, 15:5917-5928. 230843, 7565744.
42. Koranda M, Schleiffer A, Endler L, Ammerer G. Forkhead-Like Transcription Factors Recruit NddI to the Chromatin of G2/M-Specific Promoters. Nature 2000, 406:94-98. 10.1038/35017589, 10894549.
43. Loy CJ, Lydall D, Surana U. NDDI, a High-Dosage Suppressor of cdc28-I N, Is Essential for Expression of a Subset of Late-S-Phase-Specific Genes in S. cerevisiae. Molecular and Cellular Biology 1999, 19:3312-3327. 84125, 10207056.
44. Amon A, Tyers M, Futcher B, Nasmyth K. Mechanisms that Help the Yeast Cell Cycle Clock Tick: G2 Cyclins Transcriptionally Activate G2 Cyclins and Repress G1 Cyclins. Cell 1993, 74:993-1007. 10.1016/0092-8674(93)90722-3, 8402888.
45. Andrews B, Measday V. The Cyclin Family of Budding Yeast: Abundant Use of a Good Idea. Trends in Genetics 1998, 14:66-72. 10.1016/S0168-9525(97)01322-X, 9520600.
46. Schneider B, Patton E, Lanker S, Mendenhall M, Wittenberg C, Futcher B, Tyers M. Yeast GI Cyclins Are Instable in GI Phase. Nature 1998, 395:86-89. 10.1038/25774, 9738503.
47. Toyn JH, Johnson AL, Donovan JD, Toone WM, Johnston LH. The Swi5 Transcription Factor of Saccharomyces cerevisiae Has a Role in Exit from Mitosis through Induction of the Cdk-Inhibitor SicI in Telophase. Genetics 1997, 145:85-96. 1207787, 9017392.
48. Prinz S, Hwang ES, Visintin R, Amon A. The Regulation of Cdc20 Proteolysis Reveals a Role for the APC Components Cdc23 and Cdc27 during S Phase and Early Mitosis. Current Biology 1998, 8:750-760. 10.1016/S0960-9822(98)70298-2, 9651679.
49. Igual JC, Toone WM, Johnston LH. A Genetic Screen Reveals a Role for the Late G1-Specific Transcription Factor Swi4p in Diverse Cellular Functions Including Cytokinesis. J Cell Science 1997, 110:1647-1654.
50. Ronen M, Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc Natl Acad Sci USA 2006, 103(Suppl 2):389-94. 1326188, 16381818.
51. Lai LC, Kosorukoff AL, Burke PV, Kwast KE. Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 2005, 25(Suppl 10):4075-91. 1087712, 15870279.
52. Pramila T, Miles S, GuhaThakurta D, Jemiolo D, Breeden LL. Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev 2002, 16(Suppl 23):3034-45. 187489, 12464633.
53. Pramila T, Wu W, Miles S, Noble WS, Breeden LL. The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev 2006, 20(Suppl 16):2266-78. 1553209, 16912276.
54. Sapra AK, Arava Y, Khandelia P, Vijayraghavan U. Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Biol Chem 2004, 279(Suppl 50):52437-46.
55. Barrett T, Edgar R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 2006, 411:352-369. 1619900, 16939800.
56. Oba S, Sato M, Takemasa I, Monden M, Matsubara K, Ishii S. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 2003, 19(Suppl 16):2088-2096.
57. Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz S, Tainsky M. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design, and Onto-Translate. Nuc Acids Res 2003, 31(Suppl 13):3775-3781.