A multilevel data integration resource for breast cancer study

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Mosca, Ettore ^a   Alfieri, Roberta ^a   Merelli, Ivan ^a   Viti, Federica ^a   Calabria, Andrea ^a   Milanesi, Luciano ^a  

^a INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; BREAST TUMOR; FEMALE; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; METHODOLOGY; SYSTEMS BIOLOGY;

BREAST NEOPLASMS; DATABASES, GENETIC; FEMALE; HUMANS; INTERNET; MODELS, BIOLOGICAL; RESEARCH DESIGN; SYSTEMS BIOLOGY;

EID: 77953015096     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-76     Document Type: Article

References (44)

1. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000, 100:57-70. 10.1016/S0092-8674(00)81683-9, 10647931.
2. Kitano H. Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 2004, 4(3):227-235. 10.1038/nrc1300, 14993904.
3. Zucchi I, Mento E, Kuznetsov VA, Scotti M, Valsecchi V, Simionati B, Vicinanza E, Valle G, Pilotti S, Reinbold R, Vezzoni P, Albertini A, Dulbecco R. Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis. Proc Natl Acad Sci USA 2004, 101(52):18147-18152. 10.1073/pnas.0408260101, 539802, 15608061.
4. Cocola C, Sanzone S, Astigiano S, Pelucchi P, Piscitelli E, Vilardo L, Barbieri O, Bertoli G, Reinbold RA, Zucchi I. A rat mammary gland cancer cell with stem cell properties of self-renewal and multi-lineage differentiation. Cytotechnology 2008, 58:25-32. 10.1007/s10616-008-9173-9, 2593761,2593761, 19034680.
5. Mosca E, Bertoli G, Piscitelli E, Vilardo L, Reinbold RA, Zucchi I, Milanesi L. Identification of functionally related genes using data mining and data integration: a breast cancer case study. BMC Bioinformatics 2009, 10:S8. 10.1186/1471-2105-10-S12-S8, 2762073, 19828084.
6. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007, 9(2):166-180. 10.1593/neo.07112, 1813932, 17356713.
7. Tumor Gene Family Databases (TGDBs). , http://www.tumor-gene.org/tgdf.html
8. BreastCancerDatabase. , http://www.breastcancerdatabase.org
9. Szabo C, Masiello A, Ryan JF, Brody LC. The breast cancer information core: database design, structure, and scope. Hum Mutat 2000, 16(2):123-131. 10.1002/1098-1004(200008)16:2<123::AID-HUMU4>3.0.CO;2-Y, 10923033.
10. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, (37 Database):D5-15.
11. UniProtConsortium The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009, (37 Database):D169-D174. 2686606, 18836194, 10.1093/nar/gkn664, UniProtConsortium.
12. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, (37 Database):D211-D215. 10.1093/nar/gkn785, 2686546, 18940856.
13. Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007, (35 Database):D301-D303. 10.1093/nar/gkl971, 1669775, 17142228.
14. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, (37 Database):D868-D872. 10.1093/nar/gkn889, 2686529, 19015125.
15. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, (35 Database):D766-D770. 10.1093/nar/gkl1019, 1781111, 17182626.
16. Aoki-Kinoshita KF, Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007, 396:71-91. full_text, 18025687.
17. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, (37 Database):D619-D622. 10.1093/nar/gkn863, 2686536, 18981052.
18. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008, (36 Database):D637-640. 2238873, 18000002.
19. Alfieri R, Merely I, Mosca E, Milanese L. The cell cycle DB: a systems biology approach to cell cycle analysis. Nucleic Acids Res 2008, (36 Database):D641-D645. 2238882, 18160409.
20. TheGeneOntologyConsortium The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. Plos Comput Biol 2009, 5(7):e1000431. 10.1371/journal.pcbi.1000431, 2699109, 19578431, TheGeneOntologyConsortium.
21. Pontén F, Jirström I, Uhlan M. The Human Protein Atlas--a tool for pathology. J Pathol 2008, 216(4):387-393. 10.1002/path.2440, 18853439.
22. Betel D, Wilson M, Gabon A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, (36 Database):D149-D153. 2238905, 18158296.
23. Algiers R, Merely I, Mosca E, Milanese L. A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst Biol 2007, 1:35. 10.1186/1752-0509-1-35, 1995223, 17678529.
24. Osborne JD, Fallow J, Hollo M, Lin SM, Kibble WA, Zhu LJ, Danila MI, Feng AG, Chisholm EL. Annotating the human genome with Disease Ontology. BMC Genomics 2009, 10(Supple 1):S6. 10.1186/1471-2164-10-S1-S6, 19594883.
25. Chang A, Sheer M, Grate A, Schomburg I, Schomburg D. BREDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 2009, (37 Database):D588-D592. 10.1093/nar/gkn820, 2686525, 18984617.
26. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol 2005, 6(2):-R21. 10.1186/gb-2005-6-2-r21, 551541, 15693950.
27. Côté RG, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006, 7:97. 10.1186/1471-2105-7-97, 1420335, 16507094.
28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
29. Khun RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Randy BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Gibardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussle D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, (37 Database):D755-D761. 10.1093/nar/gkn875, 2686463, 18996895.
30. strich IG. Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. Bioessays 2006, 28(2):199-210. 10.1002/bies.20368, 16435295.
31. Bader GD, Hogue CWV. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
32. Boube M, Joulia L, Cribbs DL, Bourbon HM. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 2002, 110(2):143-151. 10.1016/S0092-8674(02)00830-9, 12150923.
33. Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42. 10.1038/35075138, 11333967.
34. Ma H, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19(2):270-277. 10.1093/bioinformatics/19.2.270, 12538249.
35. Reis FM, Luisi S, Caneiro MM, Cobellis L, Federico M, Camargos AF, Petraglia F. Activin, inhibin and the human breast. Mol Cell Endocrinol 2004, 225(1-2):77-82. 10.1016/j.mce.2004.02.016, 15451571.
36. Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol 2007, 3:88. 10.1038/msb4100129, 1847944, 17353930.
37. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraint. Journal Molecular Biology 1993, 234:779-815.
38. Sutherland RL, Mangrove EA. Cycling and breast cancer. J Mammary Gland Biol Neoplasia 2004, 9:95-104. 10.1023/B:JOMG.0000023591.45568.77, 15082921.
39. Courjal F, Louason G, Speiser P, Katsaros D, Zeillinger R, Theillet C. Cyclic gene amplification and overexpression in breast and ovarian cancers: evidence for the selection of cyclin D1 in breast and cyclin E in ovarian tumors. Int J Cancer 1996, 69(4):247-253. 10.1002/(SICI)1097-0215(19960822)69:4<247::AID-IJC1>3.0.CO;2-X, 8797862.
40. Hosokawa Y, Arnold A. Mechanism of cyclin D1 (CCND1, PRAD1) over expression in human cancer cells: analysis of Allele-specific expression. Genes Chromosomes Cancer 1998, 22:66-71. 10.1002/(SICI)1098-2264(199805)22:1<66::AID-GCC9>3.0.CO;2-5, 9591636.
41. Swat M, Kel A, Herzel H. Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinformatics 2004, 20(10):1506-1511. 10.1093/bioinformatics/bth110, 15231543.
42. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Novère NL, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, Forum SBML. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531. 10.1093/bioinformatics/btg015, 12611808.
43. Spencer SL, Berryman MJ, García JA, Abbott D. An ordinary differential equation model for the multistep transformation to cancer. J Theor Biol 2004, 231(4):515-524. 10.1016/j.jtbi.2004.07.006, 15488528.
44. Prasad TSK, Kandasamy K, Pandey A. Human protein reference database and human proteinpedia as discovery tools for systems biology. Methods Mol Biol 2009, 577:67-79. full_text, 19718509.