Using pathway modules as targets for assay development in xenobiotic screening

Molecular BioSystems

Volumn 8, Issue 2, 2012, Pages 531-542

  Judson, Richard S ^a   Mortensen, Holly M ^a   Shah, Imran ^a   Knudsen, Thomas B ^a   Elloumi, Fathi ^b  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84855671283     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c1mb05303e     Document Type: Article

References (67)

1. C. W. Schmidt TOX 21: new dimensions of toxicity testing Environ Health Perspect 2009 117 8 A348 53
2. M. J. Keiser V. Setola J. J. Irwin C. Laggner A. I. Abbas S. J. Hufeisen N. H. Jensen M. B. Kuijer R. C. Matos T. B. Tran R. Whaley R. A. Glennon J. Hert K. L. Thomas D. D. Edwards B. K. Shoichet B. L. Roth Predicting new molecular targets for known drugs Nature 2009 462 7270 175 81
3. G. V. Paolini R. H. Shapland W. P. van Hoorn J. S. Mason A. L. Hopkins Global mapping of pharmacological space Nat. Biotechnol. 2006 24 7 805 15 (Pubitemid 44086621)
4. M. A. Yildirim K. I. Goh M. E. Cusick A. L. Barabasi M. Vidal Drug-target network Nat. Biotechnol. 2007 25 10 1119 26 (Pubitemid 47538114)
5. S. I. Berger R. Iyengar Network analyses in systems pharmacology Bioinformatics 2009 25 19 2466 72
6. H. K. Hamadeh P. R. Bushel S. Jayadev O. DiSorbo L. Bennett L. Li R. Tennant R. Stoll J. C. Barrett R. S. Paules K. Blanchard C. A. Afshari Prediction of Compound Signature Using High Density Gene Expression Profiling Toxicol. Sci. 2002a 67 2 232 240 (Pubitemid 34746476)
7. H. K. Hamadeh P. R. Bushel S. Jayadev K. Martin O. DiSorbo S. Sieber L. Bennett R. Tennant R. Stoll J. C. Barrett K. Blanchard R. S. Paules C. A. Afshari Gene Expression Analysis Reveals Chemical-Specific Profiles Toxicol. Sci. 2002b 67 2 219 231 (Pubitemid 34746475)
8. I. Dinu J. D. Potter T. Mueller Q. Liu A. J. Adewale G. S. Jhangri G. Einecke K. S. Famulski P. Halloran Y. Yasui Gene-set analysis and reduction Briefings Bioinf. 2009 10 1 24 34
9. L. Fokkens B. Snel Cohesive versus flexible evolution of functional modules in eukaryotes PLoS Comput. Biol. 2009 5 1 e1000276
10. C. von Mering E. M. Zdobnov S. Tsoka F. D. Ciccarelli J. B. Pereira-Leal C. A. Ouzounis P. Bork Genome evolution reveals biochemical networks and functional modules Proc. Natl. Acad. Sci. U. S. A. 2003 100 26 15428 33 (Pubitemid 38021006)
11. L. H. Hartwell J. J. Hopfield S. Leibler A. W. Murray From molecular to modular cell biology Nature 1999 402 6761 suppl. C47 52
12. B. Snel P. Bork M. A. Huynen The identification of functional modules from the genomic association of genes Proc. Natl. Acad. Sci. U. S. A. 2002 99 9 5890 5 (Pubitemid 34493235)
13. J. M. Stuart E. Segal D. Koller S. K. Kim A gene-coexpression network for global discovery of conserved genetic modules Science 2003 302 5643 249 55 (Pubitemid 37248749)
14. Z. Bar-Joseph G. K. Gerber T. I. Lee N. J. Rinaldi J. Y. Yoo F. Robert D. B. Gordon E. Fraenkel T. S. Jaakkola R. A. Young D. K. Gifford Computational discovery of gene modules and regulatory networks Nat. Biotechnol. 2003 21 11 1337 42 (Pubitemid 37356619)
15. E. Segal N. Friedman D. Koller A. Regev A module map showing conditional activity of expression modules in cancer Nat. Genet. 2004 36 10 1090 8 (Pubitemid 41184471)
16. E. Segal M. Shapira A. Regev D. Pe'er D. Botstein D. Koller N. Friedman Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat. Genet. 2003 34 2 166 76 (Pubitemid 36666927)
17. E. Segal R. Yelensky D. Koller Genome-wide discovery of transcriptional modules from DNA sequence and gene expression Bioinformatics 2003 19 suppl. 1 i273 82
18. P. Uetz L. Giot G. Cagney T. A. Mansfield R. S. Judson J. R. Knight D. Lockshon V. Narayan M. Srinivasan P. Pochart A. Qureshi-Emili Y. Li B. Godwin D. Conover T. Kalbfleisch G. Vijayadamodar M. Yang M. Johnston S. Fields J. M. Rothberg A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 6770 623 7 (Pubitemid 30103994)
19. J. T. Dudley R. Tibshirani T. Deshpande A. J. Butte Disease signatures are robust across tissues and experiments Mol. Syst. Biol. 2009 5 307
20. A. V. Singh K. B. Knudsen T. B. Knudsen Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM) Reprod. Toxicol. 2005 19 3 421 39 (Pubitemid 40431235)
21. M. R. Fielden R. Brennan J. Gollub A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals Toxicol. Sci. 2007 99 1 90 100 (Pubitemid 47250370)
22. M. R. Fielden B. P. Eynon G. Natsoulis K. Jarnagin D. Banas K. L. Kolaja A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity Toxicol. Pathol. 2005 33 6 675 83 (Pubitemid 43154594)
23. R. Judson A. M. Richard D. J. Dix K. Houck M. T. Martin R. J. Kavlock V. Dellarco T. Henry T. Holderman P. Sayre S. Tan T. Carpenter E. Smith The Toxicity Data Landscape for Environmental Chemicals Environ. Health. Perspect. 2009 117 685 695
24. J. Inglese D. S. Auld A. Jadhav R. L. Johnson A. Simeonov A. Yasgar W. Zheng C. P. Austin Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries Proc. Natl. Acad. Sci. U. S. A. 2006 103 31 11473 8 (Pubitemid 44182476)
25. J. Inglese R. L. Johnson A. Simeonov M. Xia W. Zheng C. P. Austin D. S. Auld High-throughput screening assays for the identification of chemical probes Nat. Chem. Biol. 2007 3 8 466 79 (Pubitemid 47080373)
26. A. P. Davis C. G. Murphy C. A. Saraceni-Richards M. C. Rosenstein T. C. Wiegers C. J. Mattingly Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks Nucleic Acids Res. 2009 37 Database issue D786 92
27. C. J. Mattingly M. C. Rosenstein A. P. Davis G. T. Colby J. N. Forrest J. L. Boyer, Jr. The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks Toxicol. Sci. 2006 92 2 587 95 (Pubitemid 44018974)
28. B. Linghu E. Snitkin Z. Hu Y. Xia C. DeLisi Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network GenomeBiology 2009 10 9 R91
29. K. I. Goh M. E. Cusick D. Valle B. Childs M. Vidal A. L. Barabasi The human disease network Proc. Natl. Acad. Sci. U. S. A. 2007 104 21 8685 90 (Pubitemid 47175372)
30. A. L. Hopkins C. R. Groom The druggable genome Nat. Rev. Drug Discovery 2002 1 9 727 30 (Pubitemid 37361545)
31. M. Kanehisa S. Goto S. Kawashima A. Nakaya The KEGG databases at GenomeNet Nucleic Acids Res. 2002 30 1 42 6
32. M. Kanehisa M. Araki S. Goto M. Hattori M. Hirakawa M. Itoh T. Katayama S. Kawashima S. Okuda T. Tokimatsu Y. Yamanishi KEGG for linking genomes to life and the environment Nucleic Acids Res 2008 36 Database issue D480 4
33. M. Kanehisa S. Goto M. Hattori K. F. Aoki-Kinoshita M. Itoh S. Kawashima T. Katayama M. Araki M. Hirakawa From genomics to chemical genomics: new developments in KEGG Nucleic Acids Res. 2006 34 Database issue D354 7
34. H. W. Ma J. Buer A. P. Zeng Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach BMC Bioinformatics 2004 5 199
35. Y. Sun M. S. Kamel A. K. C. Wong Y. Wang Cost-sensitive boosting for classification of imbalanced data Pattern Recognit. 2007 40 12 3358 3378 (Pubitemid 47223287)
36. P. Erdos A. Renyi On the evolution of random graphs Publ. Math. Inst. Hungar. Acad. Sci 1960 5 17 61
37. D. Peck E. D. Crawford K. N. Ross K. Stegmaier T. R. Golub J. Lamb A method for high-throughput gene expression signature analysis GenomeBiology 2006 7 7 R61
38. Broad Institute Library of Integrated Network-based Cellular Signatures (LINCS). http://www.broadinstitute.org/LINCS/dataanalysis.html (accessed 7 October 2011)
39. Broad Institute Landmark Genes. http://www.broadinstitute.org/LINCS/ files/landmark-genes.htm (accessed 7 October 2011)
40. C. Huttenhower A. I. Flamholz J. N. Landis S. Sahi C. L. Myers K. L. Olszewski M. A. Hibbs N. O. Siemers O. G. Troyanskaya H. A. Coller Nearest Neighbor Networks: clustering expression data based on gene neighborhoods BMC Bioinformatics 2007 8 250
41. I. Ulitsky R. Shamir Identification of functional modules using network topology and high-throughput data BMC Syst. Biol. 2007 1 8
42. M. Manioudaki, E. Tzamali, M. Reczko and P. Poirazi, Methods for strucutural inference and functional module identification in nitracellular networks, in Bioinformatics for Systems Biology, ed., S. Krawetz, Humana Press, New York, 2009, pp. 517-539
43. P. Hernandez J. Huerta-Cepas D. Montaner F. Al-Shahrour J. Valls L. Gomez G. Capella J. Dopazo M. A. Pujana Evidence for systems-level molecular mechanisms of tumorigenesis BMC Genomics 2007 8 185
44. J. M. Schwartz J. C. Nacher Local and global modes of drug action in biochemical networks BMC Chem. Biol. 2009 9 4
45. S. Kohler S. Bauer D. Horn P. N. Robinson Walking the interactome for prioritization of candidate disease genes Am. J. Hum. Genet. 2008 82 949 958
46. T. Yu An exploratory data analysis method to reveal modular latent structures in high-throughput data BMC Bioinformatics 2010 11 440
47. L. Chen H. Wang L. Zhang W. Li Q. Wang Y. Shang Y. He W. He X. Li J. Tai Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks BMC Bioinformatics 2010 11 392
48. J. Gu Y. Chen S. Li Y. Li Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis BMC Syst. Biol. 2010 4 47
49. J. Reimand L. Tooming H. Peterson P. Adler J. Vilo GraphWeb: mining heterogeneous biological networks for gene modules with functional significance Nucleic Acids Res. 2008 36 Web Server issue W452 9
50. E. Segal M. Shapira A. Regev D. Pe'er D. Botstein D. Koller N. Friedman Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat. Genet. 2003 34 2 166 176 (Pubitemid 36666927)
51. I. Ulitsky R. Shamir Identifying functional modules using expression profiles and confidence-scored protein interactions Bioinformatics 2009 25 9 1158 64
52. M. T. Dittrich G. W. Klau A. Rosenwald T. Dandekar T. Muller Identifying functional modules in protein-protein interaction networks: an integrated exact approach Bioinformatics 2008 24 13 i223 31
53. Z. Wu X. Zhao L. Chen Identifying responsive functional modules from protein-protein interaction network Mol. Cells 2009 27 3 271 7
54. R. P. Alexander P. M. Kim T. Emonet M. B. Gerstein Understanding modularity in molecular networks requires dynamics Sci. Signaling 2009 2 81 pe44
55. I. A. Maraziotis K. Dimitrakopoulou A. Bezerianos An in silico method for detecting overlapping functional modules from composite biological networks BMC Syst. Biol. 2008 2 93
56. Z. Guo L. Wang Y. Li X. Gong C. Yao W. Ma D. Wang J. Zhu M. Zhang D. Yang S. Rao J. Wang Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network Bioinformatics 2007 23 16 2121 8 (Pubitemid 47394112)
57. A. Jaimovich R. Rinott M. Schuldiner H. Margalit N. Friedman Modularity and directionality in genetic interaction maps Bioinformatics 2010 26 12 i228 36
58. J. A. Parkkinen S. Kaski Searching for functional gene modules with interaction component models BMC Syst. Biol. 2010 4 4
59. H. Wu F. Mao Z. Su V. Olman Y. Xu Prediction of functional modules based on gene distributions in microbial genomes Genome. Inform. 2005 16 2 247 59
60. H. Wu Z. Su F. Mao V. Olman Y. Xu Prediction of functional modules based on comparative genome analysis and Gene Ontology application Nucleic Acids Res. 2005 33 9 2822 37 (Pubitemid 41511222)
61. X. Hu F. X. Wu Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks BMC Bioinformatics 2007 8 324
62. J. Song M. Singh How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 2009 25 23 3143 50
63. A. W. Rives T. Galitski Modular organization of cellular networks Proc. Natl. Acad. Sci. U. S. A. 2003 100 3 1128 33 (Pubitemid 36183967)
64. V. Spirin L. A. Mirny Protein complexes and functional modules in molecular networks Proc. Natl. Acad. Sci. U. S. A. 2003 100 21 12123 8 (Pubitemid 37271525)
65. M. Kanehisa The KEGG database Novartis Found. Symp. 2002 247 91 101
66. R. S. Judson K. A. Houck R. J. Kavlock K. B. Knudsen M. T. Martin H. M. Mortensen D. M. Reif A. M. Richard D. M. Rotroff I. Shah D. J. Dix Predictive In vitro Screening of Environmental Chemicals-The ToxCast Project Environ. Health Perspect. 2010 118 4 485 492
67. L. Shi G. Campbell W. D. Jones F. Campagne Z. Wen S. J. Walker Z. Su T. M. Chu F. M. Goodsaid L. Pusztai J. D. Shaughnessy, Jr. A. Oberthuer R. S. Thomas R. S. Paules M. Fielden B. Barlogie W. Chen P. Du M. Fischer C. Furlanello B. D. Gallas X. Ge D. B. Megherbi W. F. Symmans M. D. Wang J. Zhang H. Bitter B. Brors P. R. Bushel M. Bylesjo M. Chen J. Cheng J. Chou T. S. Davison M. Delorenzi Y. Deng V. Devanarayan D. J. Dix J. Dopazo K. C. Dorff F. Elloumi J. Fan S. Fan X. Fan H. Fang N. Gonzaludo K. R. Hess H. Hong J. Huan R. A. Irizarry R. Judson D. Juraeva S. Lababidi C. G. Lambert L. Li Y. Li Z. Li S. M. Lin G. Liu E. K. Lobenhofer J. Luo W. Luo M. N. McCall Y. Nikolsky G. A. Pennello R. G. Perkins R. Philip V. Popovici N. D. Price F. Qian A. Scherer T. Shi W. Shi J. Sung D. Thierry-Mieg J. Thierry-Mieg V. Thodima J. Trygg L. Vishnuvajjala S. J. Wang J. Wu Y. Wu Q. Xie W. A. Yousef L. Zhang X. Zhang S. Zhong Y. Zhou S. Zhu D. Arasappan W. Bao A. B. Lucas F. Berthold R. J. Brennan A. Buness J. G. Catalano C. Chang R. Chen Y. Cheng J. Cui W. Czika F. Demichelis X. Deng D. Dosymbekov R. Eils Y. Feng J. Fostel S. Fulmer-Smentek J. C. Fuscoe L. Gatto W. Ge D. R. Goldstein L. Guo D. N. Halbert J. Han S. C. Harris C. Hatzis D. Herman J. Huang R. V. Jensen R. Jiang C. D. Johnson G. Jurman Y. Kahlert S. A. Khuder M. Kohl J. Li M. Li Q. Z. Li S. Li J. Liu Y. Liu Z. Liu L. Meng M. Madera F. Martinez-Murillo I. Medina J. Meehan K. Miclaus R. A. Moffitt D. Montaner P. Mukherjee G. J. Mulligan P. Neville T. Nikolskaya B. Ning G. P. Page J. Parker R. M. Parry X. Peng R. L. Peterson J. H. Phan B. Quanz Y. Ren S. Riccadonna A. H. Roter F. W. Samuelson M. M. Schumacher J. D. Shambaugh Q. Shi R. Shippy S. Si A. Smalter C. Sotiriou M. Soukup F. Staedtler G. Steiner T. H. Stokes Q. Sun P. Y. Tan R. Tang Z. Tezak B. Thorn M. Tsyganova Y. Turpaz S. C. Vega R. Visintainer J. von Frese C. Wang E. Wang J. Wang W. Wang F. Westermann J. C. Willey M. Woods S. Wu N. Xiao J. Xu L. Xu L. Yang X. Zeng M. Zhang C. Zhao R. K. Puri U. Scherf W. Tong R. D. Wolfinger The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models Nat. Biotechnol. 2010 28 8 827 38