An information-flow-based model with dissipation, saturation and direction for active pathway inference

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Ren, Xianwen ^a   Zhou, Xiaobo ^b   Wu, Ling Yun ^a   Zhang, Xiang Sun ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; PROTEOME;

ARTICLE; BIOLOGICAL MODEL; GENE REGULATORY NETWORK; GENETICS; GENOME; INFORMATION SCIENCE; METABOLISM; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; YEAST;

GENE REGULATORY NETWORKS; GENOME; INFORMATION SCIENCE; MITOGEN-ACTIVATED PROTEIN KINASES; MODELS, BIOLOGICAL; PROGRAMMING, LINEAR; PROTEOME; SIGNAL TRANSDUCTION; YEASTS;

EID: 77952693901     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-72     Document Type: Article

References (26)

1. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008, 24:408-415. 10.1016/j.tig.2008.06.001, 2583071, 18597885.
2. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, et al. Genetics of gene expression and its effect on disease. Nature 2008, 452:423-U422. 10.1038/nature06758, 18344981.
3. Chen YQ, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang CS, Lamb J, Edwards S, Sieberts SK, et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008, 452:429-435. 10.1038/nature06757, 2841398, 18344982.
4. Smith EN, Kruglyak L. Gene-Environment Interaction in Yeast Gene Expression. PLoS Biology 2008, 6:e83. 10.1371/journal.pbio.0060083, 2292755,2292755, 18416601.
5. Workman CT, Mak HC, McCuine S, Tagne J-B, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A Systems Approach to Mapping DNA Damage Response Pathways. Science 2006, 312:1054-1059. 10.1126/science.1122088, 2811083, 16709784.
6. Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. Journal of Computational Biology 2006, 13:133-144. 10.1089/cmb.2006.13.133, 16597231.
7. Steffen M, Petti A, Aach J, D'Haeseleer P, Church G. Automated modelling of signal transduction networks. BMC Bioinformatics 2002, 3:34. 10.1186/1471-2105-3-34, 137599, 12413400.
8. Zhao X-M, Wang R-S, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucl Acids Res 2008, 36:e48. 10.1093/nar/gkn145, 2396433, 18411207.
9. Zhao XM, Wang RS, Chen L, Aihara K. Automatic modeling of signaling pathways by network flow model. J Bioinform Comput Biol 2009, 7:309-322. 10.1142/S0219720009004138, 19340917.
10. Tu Z, Wang L, Arbeitman MN, Chen T, Sun F. An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics 2006, 22:e489-496. 10.1093/bioinformatics/btl234, 16873511.
11. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol 2008, 4. 10.1038/msb.2008.4, 2290938, 18319721.
12. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Acids Res 2000, 28:27-30.
13. Xenarios C, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the Database of Interacting Proteins. Nucl Acids Res 2000, 28:289-291. 10.1093/nar/28.1.289, 102387, 10592249.
14. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau W-C, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO: mining millions of expression profiles--database and tools. Nucl Acids Res 2005, 33:D562-566. 10.1093/nar/gki022, 539976, 15608262.
15. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The Transcriptional Program of Sporulation in Budding Yeast. Science 1998, 282:699-705. 10.1126/science.282.5389.699, 9784122.
16. Brem RB, Kruglyak L. The landscape of genetic complexity across 5700 gene expression traits in yeast. Proc Natl Acad Sci USA 2005, 102:1572-1577. 10.1073/pnas.0408709102, 547855, 15659551.
17. Lockhart SR, Rymond BC. Commitment of yeast pre-mRNA to the splicing pathway requires a novel U1 small nuclear ribonucleoprotein polypeptide, Prp39p. Mol Cell Biol 1994, 14:3623-3633. 358730, 8196608.
18. Chasse SA, Flanary P, Parnell SC, Hao N, Cha JY, Siderovski DP, Dohlman HG. Genome-Scale Analysis Reveals Sst2 as the Principal Regulator of Mating Pheromone Signaling in the Yeast Saccharomyces cerevisiae. Eukaryotic Cell 2006, 5:330-346. 10.1128/EC.5.2.330-346.2006, 1405904, 16467474.
19. Bourens M, Panozzo C, Nowacka A, Imbeaud S, Mucchielli M-H, Herbert CJ. Mutations in the Saccharomyces cerevisiae Kinase Cbk1p Lead to a Fertility Defect That Can Be Suppressed by the Absence of Brr1p or Mpt5p (Puf5p), Proteins Involved in RNA Metabolism. Genetics 2009, 183:161-173. 10.1534/genetics.109.105130, 2746141, 19546315.
20. Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:231-237. 10.1038/nature01258, 12432408.
21. Zhang J, Maslov S, Shakhnovich EI. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 2008, 4. 10.1038/msb.2008.48, 2538908, 18682700.
22. Elion EA. SIGNAL TRANSDUCTION: Routing MAP Kinase Cascades. Science 1998, 281:1625-1626. 10.1126/science.281.5383.1625, 9767029.
23. Shinar G, Feinberg M. Structural Sources of Robustness in Biochemical Reaction Networks. Science 327:1389-1391. 10.1126/science.1183372, 20223989.
24. Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucl Acids Res 2002, 30:42-46. 10.1093/nar/30.1.42, 99091, 11752249.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
26. 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.