Disease pathways at the Rat Genome Database Pathway Portal: Genes in context-a network approach to understanding the molecular mechanisms of disease

Human Genomics

Volumn 8, Issue 1, 2014, Pages

  Petri, Victoria ^a   Hayman, G Thomas ^a   Tutaj, Marek ^a   Smith, Jennifer R ^a   Laulederkind, Stanley J F ^a   Wang, Shur Jen ^a   Nigam, Rajni ^a   Pons, Jeff De ^a   Shimoyama, Mary ^a   Dwinell, Melinda R ^a   Worthey, Elizabeth A ^a   Jacob, Howard J ^a  

^a MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

Altered pathway; Disease pathway; Molecular pathway; Ontology; Systems biology

Indexed keywords

4,4' ISOPROPYLIDENEDIPHENOL; AXITINIB; CISPLATIN; ESTROGEN;

ARTICLE; CARCINOGENESIS; DISEASES; ESTROGEN ACTIVITY; GENE; GENE FUNCTION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC DATABASE; HUMAN; KIDNEY CARCINOMA; METABOLISM; MOLECULAR GENETICS; MOLECULAR PATHOLOGY; NONHUMAN; PANCREAS CANCER; PHENOTYPE; PROSTATE CANCER; SIGNAL TRANSDUCTION; ANIMAL; COMPUTER INTERFACE; DISEASE MODEL; FEMALE; GENETICS; GENOME; MALE; PROCEDURES; RAT; SYSTEMS BIOLOGY;

ANIMALS; DATABASES, GENETIC; DISEASE MODELS, ANIMAL; FEMALE; GENE REGULATORY NETWORKS; GENOME; MALE; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; RATS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 84964312855     PISSN: 14739542     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/s40246-014-0017-8     Document Type: Article

References (48)

1. Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ: The Pathway Ontology - updates and applications. J Biomed Semantics 2014, 5(1):7.
2. Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, De Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ: The Rat Genome Database 2013 - data, tools and users. Brief Bioinform 2013, 14(4):520-526.
3. Rat Genome Database. http://rgd.mcw.edu.
4. Petri V: Pathway resources at the Rat Genome Database: a dynamic platform for integrating gene, pathway and disease information. In Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications. Edited by Liu LA, Wei D, Li Y, Lei H. Hershey: IGI Global; 2011:316-336.
5. Petri V, Shimoyama M, Hayman GT, Smith JR, De Pons J, Dwinell MR, Munzenmaier DH, Twigger SM, Jacob HJ, REG Team: The Rat Genome Database pathway portal. Database (Oxford) 2011. http://dx.doi.org/10.1093/database/bar010.
6. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH: PID: the pathway interaction database. Nucleic Acids Res 2010, 38 (Database issue):D355-D360.
7. Kanehisha M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40 (Database issue):D109-D114.
8. KEGG: Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/.
9. Garraway LA, Lander ES: Lessons from the cancer genome. Cell 2013, 153(1):17-37.
10. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW: Cancer genome landscapes. Science 2013, 339(6127):1546-1558.
11. Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674.
12. Srivastava SK, Arora S, Singh S, Bhardwaj A, Averett C, Singh AP: MicroRNAs in pancreatic malignancy: progress and promises. Cancer Lett 2014, 347(2):167-174.
13. Van Der Sijde MR, Ng A, Fu J: Systems genetics: from GWAS to disease pathways. Biochim Biophys Acta 2014, S0925-4439(14):00112-00114.
14. Werner HM, Mills GB, Ram PT: Cancer systems biology: a peek into the future of patient care? Nat Rev Clin Oncol 2014, 11(3):167-176.
15. CTD: Comparative Toxicogenomics Database. http://www.ctdbase.org.
16. Smith JR, Park CA, Nigam R, Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Petri V, De Pons J, Tutaj M, Liu W, Jayaraman P, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. J Biomed Semantics 2013, 4(1):26.
17. SMPDB: Small Molecule Pathway Database. http://www.smpdb.ca/.
18. Reactome. http://www.reactome.org/.
19. Gnoni A, Licchetta A, Scarpa A, Azzariti A, Brunetti AE, Simone G, Nardulli P, Santini D, Aieta M, Delcuratolo S, Silvestris N: Carcinogenesis of pancreatic adenocarcinoma: precursor lesions. Int J Mol Sci 2013, 14:19731-19762.
20. Bryant KL, Mancias JD, Kimmelamn AC, der CJ: KRAS: feeding pancreatic cancer proliferation. Trends Bioch Sci 2014, 39(2):91-100.
21. Eser S, Schnieke A, Schneider G, Saur D: Oncogenic KRAS signaling in pancreatic cancer. Br J Cancer 2014. http:/dx.doi.org/10.1038/bjc.2014.215.
22. Sherr CJ: The Pezcoller lecture: cancer cell cycles revisited. Cancer Res 2000, 60(14):3689-3695.
23. Maggi LB Jr, Winkeler CL, Miceli AP, Apicelli AJ, Brady SN, Kuchenreuther MJ, Weber JD: ARF tumor suppression in the nucleolus. Biochim Biophys Acta 2014, 1842(6):831-839.
24. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky T, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Doanue C, Eshleman JR, Kern SE, Hruban RH, et al: Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321(5897):1801-1806.
25. Wong HH, Lemoine NR: Pancreatic cancer: molecular pathogenesis and new therapeutics. Nat Rev Gastroenterol Hepatol 2009, 6(7):412-422.
26. Yachida S, Iacobuzio-Donahue CA: Evolution and dynamics of pancreatic cancer progression. Oncogene 2013, 32(45):5253-5260.
27. Stephen AG, Esposito D, Bagni RK, McCormick F: Dragging Ras back in the ring. Cancer Cell 2014, 25(3):272-280.
28. Fukushige S, Horii A: Road to early detection of pancreatic cancer: attempts to utilize epigenetic biomarkers. Cancer Lett 2014, 342(2):231-237.
29. Barbieri CE, Bangma CH, Bjartell A, Catto J W F, Culig Z, Gronberg H, Luo J, Visakorpi T, Rubin MA: The mutational landscape of prostate cancer. Eur Urol 2013, 64(4):567-576.
30. Devlin HL, Mudryi M: Progression of prostate cancer: multiple pathways to androgen independence. Cancer Lett 2009, 274(2):177-186.
31. Vis AN, Schroder FH: Key targets of hormonal treatment of prostate cancer. Part 1: the androgen receptor and steroidogenic pathways. BJU Int 2009, 104(4):438-448.
32. Itkonen H, Mills IG: Chromatin binding by the androgen receptor in prostate cancer. Mol Cell Endocrinol 2012, 360(1-2):44-51.
33. Chng KR, Cheung W: Sequencing the transcriptional network of androgen receptor in prostate cancer. Cancer Lett 2013, 340(2):254-260.
34. McCarthy MF, Hejazi J, Rastmanesh R: Beyond androgen deprivation: ancillary integrative strategies for targeting the androgen receptor addiction of prostate cancer. Sage J 2014. http://dx.doi.org/10.1177/1534735414534728.
35. Audenet F, Yates DR, Cance-Tassin G, Cussenot O, Roupret M: Genetic pathways involved in the carcinogenesis of clear cell renal cell carcinoma: genomics towards personalized medicine. BJU Int 2012, 109(12):1864-1870.
36. Semenza GL: Hypoxia-inducible factors in physiology and medicine. Cell 2012, 148(3):399-408.
37. Keefe SM, Nathanson KL, Rathmell WK: The molecular biology of renal cell carcinoma. Semin Oncol 2013, 40(4):421-428.
38. Pawlus MR, Hu CJ: Enhanceosomes as integrators of hypoxia inducible factor (HIF) and other transcription factors in the hypoxic transcriptional response. Cell Signal 2013, 25(9):1895-1903.
39. Haase VH: Renal cancer: oxygen meets metabolism. Exp Cell Res 2012, 318:1057-1067.
40. Brocato J, Chervona Y, Costa M: Molecular responses to hypoxia-inducible factor 1alpha and beyond. Mol Pharmacol 2014, 85(5):651-657.
41. Pena-Llopis S, Christie A, Xie XJ, Brugarolas J: Cooperation and antagonism among cancer genes: the renal cancer paradigm. Cancer Res 2013, 73(14):4173-4179.
42. Robinson CM, Ohh M: The multifaceted von Hippel-Lindau tumour suppressor protein. FEBS Lett 2014, 588(16):2704-2711.
43. Ciarimboli G: Membrane transporters as mediators of cisplatin effects and side effects. Scientifica (Cairo) 2012. http://dx.doi.org/10.6064/2012/473829.
44. Rezg R, El-Fazaa S, Gharbi N, Mornagui B: Bisphenol A and human chronic diseases: current evidence, possible mechanisms, and future perspectives. Environ Int 2014, 64:83-90.
45. Ziv O, Glaser B, Dor Y: The plastic pancreas. Dev Cell 2013, 26(1):3-7.
46. Day-Richter J, Harris MA, Haendel M, Lewis S, Gene Ontology OBO-Edit Working Group: OBO-Edit-an ontology editor for biologists. Bioinformatics (Oxford, England) 2007, 7(3):256-274.
47. Pathway Studio. http://www.elsevier.com/online-tools/pathway-studio]
48. Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M: The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information. Hum Genomics 2013, 7:4.