Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Tian, Ye ^a   Zhang, Bai ^b   Hoffman, Eric P ^c   Clarke, Robert ^d   Zhang, Zhen ^b   Shih, Ie Ming ^b   Xuan, Jianhua ^a   Herrington, David M ^e   Wang, Yue ^a  

^a Virginia Polytechnic Institute and State University   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c CHILDREN'S NATIONAL MEDICAL CENTER   (United States)

^d GEORGETOWN UNIVERSITY   (United States)

^e WAKE FOREST SCHOOL OF MEDICINE   (United States)

Author keywords

Biological networks; Convex optimization; Differential dependency network; Knowledge incorporation; Network analysis; Network rewiring; Probabilistic graphical models; Systems biology

Indexed keywords

APOPTOSIS; BIOLOGICAL MODEL; BREAST TUMOR; CELL CYCLE; CYTOLOGY; DNA MICROARRAY; GENETICS; HUMAN; METABOLISM; OXIDATIVE STRESS; PATHOLOGY; PROCEDURES; RECURRENT DISEASE; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

APOPTOSIS; BREAST NEOPLASMS; CELL CYCLE; HUMANS; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATIVE STRESS; RECURRENCE; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

EID: 84905862253     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-014-0087-1     Document Type: Article

References (41)

1. Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet 2013, 14(10):719-732. 24045689.
2. Creixell P, Schoof EM, Erler JT, Linding R. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol 2012, 30(9):842-848. 22965061.
3. Califano A. Rewiring makes the difference. Mol Syst Biol 2011, 7:463. 21245848.
4. Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011, 12(1):56-68. 21164525.
5. Ideker T, Krogan NJ: Differential network biology. Mol Syst Biol 2012, 8(1)..
6. Reverter A, Hudson NJ, Nagaraj SH, Perez-Enciso M, Dalrymple BP. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics 2010, 26(7):896-904. 20144946.
7. Hudson NJ, Dalrymple BP, Reverter A. Beyond differential expression: the quest for causal mutations and effector molecules. BMC Genomics 2012, 13:356. 22849396.
8. Shmulevich I, Dougherty ER, Kim S, Zhang W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002, 18(2):261-274. 11847074.
9. Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F. Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics 2004, 20(9):1361-1372. 14962938.
10. Tyson JJ, Baumann WT, Chen C, Verdugo A, Tavassoly I, Wang Y, Weiner LM, Clarke R. Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nat Rev Cancer 2011, 11(7):523-532. 21677677.
11. Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303(5659):799-805. 14764868.
12. Hudson NJ, Reverter A, Dalrymple BP. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 2009, 5(5):e1000382. 19412532.
13. Zhang B, Li H, Riggins RB, Zhan M, Xuan J, Zhang Z, Hoffman EP, Clarke R, Wang Y. Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics 2009, 25(4):526-532. 19112081.
14. Zhang B, Tian Y, Jin L, Li H, Shih Ie M, Madhavan S, Clarke R, Hoffman EP, Xuan J, Hilakivi-Clarke L, Wang Y. DDN: a caBIG(R) analytical tool for differential network analysis. Bioinformatics 2011, 27(7):1036-1038. 21296752.
15. Roy S, Werner-Washburne M, Lane T. A multiple network learning approach to capture system-wide condition-specific responses. Bioinformatics 2011, 27(13):1832-1838. 21551143.
16. Gill R, Datta S, Datta S. A statistical framework for differential network analysis from microarray data. BMC Bioinformatics 2010, 11:95. 20170493.
17. Emmert-Streib F. The chronic fatigue syndrome: a comparative pathway analysis. J Comput Biol 2007, 14(7):961-972. 17803373.
18. Ahmed A, Xing EP. Recovering time-varying networks of dependencies in social and biological studies. Proc Natl Acad Sci 2009, 106(29):11878-11883. 19570995.
19. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10592173.
20. Wang Z, Xu W, San Lucas FA, Liu Y. Incorporating prior knowledge into Gene Network Study. Bioinformatics 2013, 29(20):2633-2640. 23956306.
21. Zhang B, Wang Y: Learning Structural Changes of Gaussian Graphical Models in Controlled Experiments. In Uncertainty in Artificial Intelligence (UAI 2010). 2010..
22. Tian Y, Zhang B, Shih I-M, Wang Y: Knowledge-Guided Differential Dependency Network Learning for Detecting Structural Changes in Biological Networks. In ACM International Conference on Bioinformatics and Computational Biology. 2011:254-263..
23. Meinshausen N, Bu¨hlmann P. High-dimensional graphs and variable selection with the Lasso. Ann Stat 2006, 34(3):1436-1462.
24. Bunke H, Allermann G. Inexact graph matching for structural pattern recognition. Pattern Recogn Lett 1983, 1(4):245-253.
25. Ikner A, Shiozaki K. Yeast signaling pathways in the oxidative stress response. Mutat Res Fundam Mol Mech Mutagen 2005, 569(1-2):13-27.
26. Jamieson DJ. Oxidative stress responses of the yeast Saccharomyces cerevisiae. Yeast 1998, 14(16):1511-1527. 9885153.
27. Kuge S, Jones N, Nomoto A. Regulation of yAP-1 nuclear localization in response to oxidative stress. EMBO J 1997, 16(7):1710-1720. 9130715.
28. Costa VMV, Amorim MA, Quintanilha A, Moradas-Ferreira P. Hydrogen peroxide-induced carbonylation of key metabolic enzymes in Saccharomyces cerevisiae: the involvement of the oxidative stress response regulators Yap1 and Skn7. Free Radic Biol Med 2002, 33(11):1507-1515. 12446208.
29. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 2012, 40(D1):D700-D705. 22110037.
30. 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(12):4241-4257. 11102521.
31. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 2001, 12(2):323-337. 11179418.
32. Singh K: Oxidant-Induced Cell Death Mediated By A Rho Gtpase In Saccharomyces cerevisiae. PhD thesis.: The Ohio State University, Molecular Genetics Department; 2008..
33. Lee ME, Singh K, Snider J, Shenoy A, Paumi CM, Stagljar I, Park H-O. The Rho1 GTPase acts together with a vacuolar glutathione S-conjugate transporter to protect yeast cells from oxidative stress. Genetics 2011, 188(4):859-870. 21625004.
34. Petkova MI, Pujol-Carrion N, de la Torre-Ruiz MA. Signal flow between CWI/TOR and CWI/RAS in budding yeast under conditions of oxidative stress and glucose starvation. Commun Integr Biol 2010, 3(6):555-557. 21331237.
35. Grant CM, Perrone G, Dawes IW. Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the Yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 1998, 253(3):893-898. 9918826.
36. Lee J, Godon C, Lagniel G, Spector D, Garin J, Labarre J, Toledano MB. Yap1 and Skn7 control Two specialized oxidative stress response regulons in yeast. J Biol Chem 1999, 274(23):16040-16046. 10347154.
37. Tripathi S, Emmert-Streib F. Assessment method for a power analysis to identify differentially expressed pathways. PLoS One 2012, 7(5):e37510. 22629411.
38. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C. Definition of Clinically Distinct Molecular Subtypes in Estrogen Receptor-Positive Breast Carcinomas Through Genomic Grade. J Clin Oncol 2007, 25(10):1239-1246. 17401012.
39. Su Z, Xin S, Xu L, Cheng J, Guo J, Li L, Wei Q. The calcineurin B subunit induces TNF-related apoptosis-inducing ligand (TRAIL) expression via CD11b-NF-κB pathway in RAW264.7 macrophages. Biochem Biophys Res Commun 2012, 417(2):777-783. 22197822.
40. Murphy K, Ranganathan V, Farnsworth M, Kavallaris M, Lock R. Bcl-2 inhibits Bax translocation from cytosol to mitochondria during drug-induced apoptosis of human tumor cells. Cell Death Differ 2000, 7(1):102-111. 10713725.
41. Hanahan D, Weinberg Robert A. Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674. 21376230.