Annotating cancer variants and anti-cancer therapeutics in Reactome

Cancers

Volumn 4, Issue 4, 2012, Pages 1180-1211

  Milacic, Marija ^a   Haw, Robin ^a   Rothfels, Karen ^a   Wu, Guanming ^a   Croft, David ^b   Hermjakob, Henning ^b   D'Eustachio, Peter ^c   Stein, Lincoln ^a  

^a ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer annotation; EGFR signaling; Network visualization; Pathway database; Pathway visualization

Indexed keywords

1 (1 CYANO 1 METHYLETHYL) 3 METHYL 8 (3 QUINOLINYL)IMIDAZO[4,5 C]QUINOLIN 2(1H,3H) ONE; 1 TERT BUTYL 3 [6 (3,5 DIMETHOXYPHENYL) 2 (4 DIETHYLAMINOBUTYLAMINO)PYRIDO[2,3 D]PYRIMIDIN 7 YL]UREA; 3 [4 METHYL 2 (2 OXO 3 INDOLINYLMETHYLIDENYL) 3 PYRROLYL]PROPIONIC ACID; AFATINIB; ALVESPIMYCIN; AZD 4547; BRIVANIB; BRIVANIB ALANINATE; BUPARLISIB; CANERTINIB; CETUXIMAB; DOVITINIB; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB; GEFITINIB; GELDANAMYCIN; HERBIMYCIN A; LAPATINIB; LENVATINIB; MASITINIB; MIDOSTAURIN; NERATINIB; PELITINIB; PROTEIN VARIANT; RABEPRAZOLE; RETASPIMYCIN; TANESPIMYCIN; VANDETANIB;

AMINO ACID SEQUENCE; ARTICLE; CANCER RESEARCH; COMPUTER MODEL; COMPUTER NETWORK; DATA ANALYSIS SOFTWARE; DISEASE ASSOCIATION; FRAMESHIFT MUTATION; GENE DELETION; GENETIC DATABASE; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NONSENSE MUTATION; PROTEIN EXPRESSION; PROTEIN PROCESSING; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SOMATIC MUTATION;

EID: 84871602426     PISSN: None     EISSN: 20726694     Source Type: Journal    
DOI: 10.3390/cancers4041180     Document Type: Article

References (88)

1. Vogelstein, B.; Fearon, E.R.; Hamilton, S.R.; Kern, S.E.; Preisinger, A.C.; Leppert, M.; Nakamura, Y.; White, R.; Smits, A.M. et al. Genetic alterations during colorectal-tumor development. N. Engl. J. Med. 1988, 319, 525-532.
2. Shah, S.P.; Roth, A.; Goya, R.; Oloumi, A.; Ha, G.; Zhao, Y.; Turashvili, G.; Ding, J.; Tse, K.; Haffari, G. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012, 486, 395-399.
3. Hahn, S.A.; Schutte, M.; Hoque, A.T.; Moskaluk, C.A.; da Costa, L.T.; Rozenblum, E.; Weinstein, C.L.; Fischer, A.; Yeo, C.J.; Hruban, R.H. et al. DPC4, a candidate tumor suppressor gene at human chromosome 18q21.1. Science 1996, 271, 350-353.
4. Hockenbery, D.; Nunez, G.; Milliman, C.; Schreiber, R.D.; Korsmeyer, S.J. Bcl-2 is an inner mitochondrial membrane protein that blocks programmed cell death. Nature 1990, 348, 334-336.
5. Lew, D.J.; Dulic, V.; Reed, S.I. Isolation of three novel human cyclins by rescue of G1 cyclin (Cln) function in yeast. Cell 1991, 66, 1197-1206.
6. Motokura, T.; Bloom, T.; Kim, H.G.; Juppner, H.; Ruderman, J.V.; Kronenberg, H.M.; Arnold, A. A novel cyclin encoded by a bcl1-linked candidate oncogene. Nature 1991, 350, 512-515.
7. Govindan, R.; Ding, L.; Griffith, M.; Subramanian, J.; Dees, N.D.; Kanchi, K.L.; Maher, C.A.; Fulton, R.; Fulton, L.; Wallis, J. et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012, 150, 1121-1134.
8. Greenman, C.; Stephens, P.; Smith, R.; Dalgliesh, G.L.; Hunter, C.; Bignell, G.; Davies, H.; Teague, J.; Butler, A.; Stevens, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446, 153-158.
9. Croft, D.; O'Kelly, G.; Wu, G.; Haw, R.; Gillespie, M.; Matthews, L.; Caudy, M.; Garapati, P.; Gopinath, G.; Jassal, B. et al. Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Res. 2011, 39, D691-D697.
10. Matthews, L.; Gopinath, G.; Gillespie, M.; Caudy, M.; Croft, D.; de Bono, B.; Garapati, P.; Hemish, J.; Hermjakob, H.; Jassal, B. et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37, D619-D622.
11. Vastrik, I.; D'Eustachio, P.; Schmidt, E.; Gopinath, G.; Croft, D.; de Bono, B.; Gillespie, M.; Jassal, B.; Lewis, S.; Matthews, L. et al. Reactome: A knowledge base of biologic pathways and processes. Genome Biol. 2007, 8, R39.
12. Joshi-Tope, G.; Gillespie, M.; Vastrik, I.; D'Eustachio, P.; Schmidt, E.; de Bono, B.; Jassal, B.; Gopinath, G.R.; Wu, G.R.; Matthews, L. et al. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res. 2005, 33, D428-D432.
13. Gillespie, M.; Shamovsky, V.; D'Eustachio, P. Human and chicken TLR pathways: Manual curation and computer-based orthology analysis. Mamm. Genome 2010, 22, 130-138.
14. Jassal, B.; Jupe, S.; Caudy, M.; Birney, E.; Stein, L.; Hermjakob, H.; D'Eustachio, P. The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) 2010, 2010, baq018.
15. Maglott, D.; Ostell, J.; Pruitt, K.D.; Tatusova, T. Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Res. 2011, 39, D52-D57.
16. Flicek, P.; Aken, B.L.; Ballester, B.; Beal, K.; Bragin, E.; Brent, S.; Chen, Y.; Clapham, P.; Coates, G.; Fairley, S. et al. Ensembl's 10th year. Nucleic Acids Res. 2010, 38, D557-D562.
17. Consortium, T.U. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40, D71-D75.
18. Fujita, P.A.; Rhead, B.; Zweig, A.S.; Hinrichs, A.S.; Karolchik, D.; Cline, M.S.; Goldman, M.; Barber, G.P.; Clawson, H.; Coelho, A. et al. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res. 2011, 39, D876-D882.
19. De Matos, P.; Alcantara, R.; Dekker, A.; Ennis, M.; Hastings, J.; Haug, K.; Spiteri, I.; Turner, S.; Steinbeck, C. Chemical Entities of Biological Interest: An update. Nucleic Acids Res. 2010, 38, D249-D254.
20. Consortium, G.O. The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Res. 2010, 38, D331-D335.
21. Reactome-Signaling by EGFR. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9417/ (accessed on 20 September 2012).
22. Reactome-Signaling by FGFR. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9470/ (accessed on 20 September 2012).
23. Reactome-Signaling by NOTCH. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_299/ (accessed on 20 September 2012).
24. Reactome-PIP3 Activates AKT Signaling. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_75829/ (accessed on 20 September 2012).
25. Reactome-RAF/MAP Kinase Cascade. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_634/ (accessed on 20 September 2012).
26. Reactome-Apoptosis. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_578/ (accessed on 20 September 2012).
27. Reactome-Cell Cycle Checkpoints. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1538/ (accessed on 20 September 2012).
28. Reactome-Mitotic G1-G1/S phases. Available online: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21267/ (accessed on 20 September 2012).
29. Sherrill, J.M.; Kyte, J. Activation of epidermal growth factor receptor by epidermal growth factor. Biochemistry 1996, 35, 5705-5718.
30. Eswarakumar, V.P.; Lax, I.; Schlessinger, J. Cellular signaling by fibroblast growth factor receptors. Cytokine Growth Factor Rev. 2005, 16, 139-149.
31. Ferguson, K.M. Structure-based view of epidermal growth factor receptor regulation. Annu. Rev. Biophys. 2008, 37, 353-373.
32. Furdui, C.M.; Lew, E.D.; Schlessinger, J.; Anderson, K.S. Autophosphorylation of FGFR1 kinase is mediated by a sequential and precisely ordered reaction. Mol. Cell 2006, 21, 711-717.
33. Hart, K.C.; Robertson, S.C.; Donoghue, D.J. Identification of tyrosine residues in constitutively activated fibroblast growth factor receptor 3 involved in mitogenesis, Stat activation, and phosphatidylinositol 3-kinase activation. Mol. Biol. Cell 2001, 12, 931-942.
34. Mohammadi, M.; Dikic, I.; Sorokin, A.; Burgess, W.H.; Jaye, M.; Schlessinger, J. Identification of six novel autophosphorylation sites on fibroblast growth factor receptor 1 and elucidation of their importance in receptor activation and signal transduction. Mol. Cell. Biol. 1996, 16, 977-989.
35. Avraham, R.; Yarden, Y. Feedback regulation of EGFR signalling: Decision making by early and delayed loops. Nat. Rev. Mol. Cell Biol. 2011, 12, 104-117.
36. Schlessinger, J. Common and distinct elements in cellular signaling via EGF and FGF receptors. Science 2004, 306, 1506-1507.
37. Ong, S.H.; Hadari, Y.R.; Gotoh, N.; Guy, G.R.; Schlessinger, J.; Lax, I. Stimulation of phosphatidylinositol 3-kinase by fibroblast growth factor receptors is mediated by coordinated recruitment of multiple docking proteins. Proc. Natl. Acad. Sci. USA 2001, 98, 6074-6079.
38. Rodrigues, G.A.; Falasca, M.; Zhang, Z.; Ong, S.H.; Schlessinger, J. A novel positive feedback loop mediated by the docking protein Gab1 and phosphatidylinositol 3-kinase in epidermal growth factor receptor signaling. Mol. Cell. Biol. 2000, 20, 1448-1459.
39. Manning, B.D.; Cantley, L.C. AKT/PKB signaling: Navigating downstream. Cell 2007, 129, 1261-1274.
40. Burke, J.E.; Vadas, O.; Berndt, A.; Finegan, T.; Perisic, O.; Williams, R.L. Dynamics of the phosphoinositide 3-kinase p110delta interaction with p85alpha and membranes reveals aspects of regulation distinct from p110alpha. Structure 2011, 19, 1127-1137.
41. Mandelker, D.; Gabelli, S.B.; Schmidt-Kittler, O.; Zhu, J.; Cheong, I.; Huang, C.H.; Kinzler, K.W.; Vogelstein, B.; Amzel, L.M. A frequent kinase domain mutation that changes the interaction between PI3Kalpha and the membrane. Proc. Natl. Acad. Sci. USA 2009, 106, 16996-17001.
42. Maehama, T.; Dixon, J.E. The tumor suppressor, PTEN/MMAC1, dephosphorylates the lipid second messenger, phosphatidylinositol 3,4,5-trisphosphate. J. Biol. Chem. 1998, 273, 13375-13378.
43. Scheid, M.P.; Marignani, P.A.; Woodgett, J.R. Multiple phosphoinositide 3-kinase-dependent steps in activation of protein kinase B. Mol. Cell. Biol. 2002, 22, 6247-6260.
44. Hollander, M.C.; Blumenthal, G.M.; Dennis, P.A. PTEN loss in the continuum of common cancers, rare syndromes and mouse models. Nat. Rev. Cancer 2011, 11, 289-301.
45. Greulich, H.; Chen, T.H.; Feng, W.; Janne, P.A.; Alvarez, J.V.; Zappaterra, M.; Bulmer, S.E.; Frank, D.A.; Hahn, W.C.; Sellers, W.R. et al. Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants. PLoS Med. 2005, 2, e313.
46. Fernandes, H.; Cohen, S.; Bishayee, S. Glycosylation-induced conformational modification positively regulates receptor-receptor association: A study with an aberrant epidermal growth factor receptor (EGFRvIII/DeltaEGFR) expressed in cancer cells. J. Biol. Chem. 2001, 276, 5375-5383.
47. Wesche, J.; Haglund, K.; Haugsten, E.M. Fibroblast growth factors and their receptors in cancer. Biochem. J. 2011, 437, 199-213.
48. Weiss, J.; Sos, M.L.; Seidel, D.; Peifer, M.; Zander, T.; Heuckmann, J.M.; Ullrich, R.T.; Menon, R.; Maier, S.; Soltermann, A. et al. Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci. Transl. Med. 2010, 2, 62-93.
49. Turner, N.; Grose, R. Fibroblast growth factor signalling: From development to cancer. Nat. Rev. Cancer 2010, 10, 116-129.
50. Cappellen, D.; de Oliveira, C.; Ricol, D.; de Medina, S.; Bourdin, J.; Sastre-Garau, X.; Chopin, D.; Thiery, J.P.; Radvanyi, F. Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas. Nat. Genet. 1999, 23, 18-20.
51. Neilson, K.M.; Friesel, R. Ligand-independent activation of fibroblast growth factor receptors by point mutations in the extracellular, transmembrane, and kinase domains. J. Biol. Chem. 1996, 271, 25049-25057.
52. Sun, M.; Hillmann, P.; Hofmann, B.T.; Hart, J.R.; Vogt, P.K. Cancer-derived mutations in the regulatory subunit p85alpha of phosphoinositide 3-kinase function through the catalytic subunit p110alpha. Proc. Natl. Acad. Sci. USA 2010, 107, 15547-15552.
53. Jaiswal, B.S.; Janakiraman, V.; Kljavin, N.M.; Chaudhuri, S.; Stern, H.M.; Wang, W.; Kan, Z.; Dbouk, H.A.; Peters, B.A.; Waring, P. et al. Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation. Cancer Cell 2009, 16, 463-474.
54. Huang, C.H.; Mandelker, D.; Schmidt-Kittler, O.; Samuels, Y.; Velculescu, V.E.; Kinzler, K.W.; Vogelstein, B.; Gabelli, S.B.; Amzel, L.M. The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations. Science 2007, 318, 1744-1748.
55. Miled, N.; Yan, Y.; Hon, W.C.; Perisic, O.; Zvelebil, M.; Inbar, Y.; Schneidman-Duhovny, D.; Wolfson, H.J.; Backer, J.M.; Williams, R.L. Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit. Science 2007, 317, 239-242.
56. Zhao, J.J.; Liu, Z.; Wang, L.; Shin, E.; Loda, M.F.; Roberts, T.M. The oncogenic properties of mutant p110alpha and p110beta phosphatidylinositol 3-kinases in human mammary epithelial cells. Proc. Natl. Acad. Sci. USA 2005, 102, 18443-18448.
57. Carpten, J.D.; Faber, A.L.; Horn, C.; Donoho, G.P.; Briggs, S.L.; Robbins, C.M.; Hostetter, G.; Boguslawski, S.; Moses, T.Y.; Savage, S. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 2007, 448, 439-444.
58. Han, S.Y.; Kato, H.; Kato, S.; Suzuki, T.; Shibata, H.; Ishii, S.; Shiiba, K.; Matsuno, S.; Kanamaru, R.; Ishioka, C. Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay. Cancer Res. 2000, 60, 3147-3151.
59. Pao, W.; Chmielecki, J. Rational, biologically based treatment of EGFR-mutant non-small-cell lung cancer. Nat. Rev. Cancer 2010, 10, 760-774.
60. Greulich, H.; Pollock, P.M. Targeting mutant fibroblast growth factor receptors in cancer. Trends Mol. Med. 2011, 17, 283-292.
61. Liu, P.; Cheng, H.; Roberts, T.M.; Zhao, J.J. Targeting the phosphoinositide 3-kinase pathway in cancer. Nat. Rev. Drug Discov. 2009, 8, 627-644.
62. Montecchi-Palazzi, L.; Beavis, R.; Binz, P.A.; Chalkley, R.J.; Cottrell, J.; Creasy, D.; Shofstahl, J.; Seymour, S.L.; Garavelli, J.S. The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol. 2008, 26, 864-866.
63. Yun, C.H.; Boggon, T.J.; Li, Y.; Woo, M.S.; Greulich, H.; Meyerson, M.; Eck, M.J. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: Mechanism of activation and insights into differential inhibitor sensitivity. Cancer Cell 2007, 11, 217-227.
64. Urick, M.E.; Rudd, M.L.; Godwin, A.K.; Sgroi, D.; Merino, M.; Bell, D.W. PIK3R1 (p85alpha) is somatically mutated at high frequency in primary endometrial cancer. Cancer Res. 2011, 71, 4061-4067.
65. Demiroglu, A.; Steer, E.J.; Heath, C.; Taylor, K.; Bentley, M.; Allen, S.L.; Koduru, P.; Brody, J.P.; Hawson, G.; Rodwell, R. et al. The t(8;22) in chronic myeloid leukemia fuses BCR to FGFR1: Transforming activity and specific inhibition of FGFR1 fusion proteins. Blood 2001, 98, 3778-3783.
66. Forbes, S.A.; Bindal, N.; Bamford, S.; Cole, C.; Kok, C.Y.; Beare, D.; Jia, M.; Shepherd, R.; Leung, K.; Menzies, A. et al. COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011, 39, D945-D950.
67. Schriml, L.M.; Arze, C.; Nadendla, S.; Chang, Y.W.; Mazaitis, M.; Felix, V.; Feng, G.; Kibbe, W.A. Disease Ontology: A backbone for disease semantic integration. Nucleic Acids Res. 2012, 40, D940-D946.
68. De Coronado, S.; Wright, L.W.; Fragoso, G.; Haber, M.W.; Hahn-Dantona, E.A.; Hartel, F.W.; Quan, S.L.; Safran, T.; Thomas, N.; Whiteman, L. The NCI Thesaurus quality assurance life cycle. J. Biomed. Inform. 2009, 42, 530-539.
69. Lee, J.C.; Vivanco, I.; Beroukhim, R.; Huang, J.H.; Feng, W.L.; DeBiasi, R.M.; Yoshimoto, K.; King, J.C.; Nghiemphu, P.; Yuza, Y. et al. Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med. 2006, 3, e485.
70. Li, S.; Schmitz, K.R.; Jeffrey, P.D.; Wiltzius, J.J.; Kussie, P.; Ferguson, K.M. Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. Cancer Cell 2005, 7, 301-311.
71. Stebbins, C.E.; Russo, A.A.; Schneider, C.; Rosen, N.; Hartl, F.U.; Pavletich, N.P. Crystal structure of an Hsp90-geldanamycin complex: Targeting of a protein chaperone by an antitumor agent. Cell 1997, 89, 239-250.
72. Bai, A.; Meetze, K.; Vo, N.Y.; Kollipara, S.; Mazsa, E.K.; Winston, W.M.; Weiler, S.; Poling, L.L.; Chen, T.; Ismail, N.S. et al. GP369, an FGFR2-IIIb-specific antibody, exhibits potent antitumor activity against human cancers driven by activated FGFR2 signaling. Cancer Res. 2010, 70, 7630-7639.
73. Le Novere, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M.I.; Wimalaratne, S.M. et al. The Systems Biology Graphical Notation. Nat. Biotechnol. 2009, 27, 735-741.
74. Aranda, B.; Achuthan, P.; Alam-Faruque, Y.; Armean, I.; Bridge, A.; Derow, C.; Feuermann, M.; Ghanbarian, A.T.; Kerrien, S.; Khadake, J.; Kerssemakers, J. et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010, 38, D525-D531.
75. Overington, J. ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J. Comput. Aided Mol. Des. 2009, 23, 195-198.
76. Funahashi, A.; Tanimura, N.; Morohashi, M.; Kitano, H. CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. BioSilico 2003, 1, 159-162.
77. Killcoyne, S.; Carter, G.W.; Smith, J.; Boyle, J. Cytoscape: A community-based framework for network modeling. Methods Mol. Biol. 2009, 563, 219-239.
78. Junker, B.H.; Klukas, C.; Schreiber, F. VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006, 7, 109.
79. Hudson, T.J.; Anderson, W.; Artez, A.; Barker, A.D.; Bell, C.; Bernabe, R.R.; Bhan, M.K.; Calvo, F.; Eerola, I.; Gerhard, D.S. et al. International network of cancer genome projects. Nature 2010, 464, 993-998.
80. International Cancer Genome Consortium. Available online: http://www.icgc.org (accessed on 20 September 2012).
81. Caspi, R.; Altman, T.; Dale, J.M.; Dreher, K.; Fulcher, C.A.; Gilham, F.; Kaipa, P.; Karthikeyan, A.S.; Kothari, A.; Krummenacker, M. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010, 38, D473-D479.
82. Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38, D355-D360.
83. Mi, H.; Dong, Q.; Muruganujan, A.; Gaudet, P.; Lewis, S.; Thomas, P.D. PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010, 38, D204-D210.
84. Schaefer, C.F.; Anthony, K.; Krupa, S.; Buchoff, J.; Day, M.; Hannay, T.; Buetow, K.H. PID: The Pathway Interaction Database. Nucleic Acids Res. 2009, 37, D674-D679.
85. Bello, S.M.; Richardson, J.E.; Davis, A.P.; Wiegers, T.C.; Mattingly, C.J.; Dolan, M.E.; Smith, C.L.; Blake, J.A.; Eppig, J.T. Disease model curation improvements at Mouse Genome Informatics. Database (Oxford) 2012, 2012, bar063.
86. Davis, A.P.; King, B.L.; Mockus, S.; Murphy, C.G.; Saraceni-Richards, C.; Rosenstein, M.; Wiegers, T.; Mattingly, C.J. The Comparative Toxicogenomics Database: Update 2011. Nucleic Acids Res. 2011, 39, D1067-D1072.
87. Whirl-Carrillo, M.; McDonagh, E.M.; Hebert, J.M.; Gong, L.; Sangkuhl, K.; Thorn, C.F.; Altman, R.B.; Klein, T.E. Pharmacogenomics knowledge for personalized medicine. Clin. Pharmacol. Ther. 2012, 92, 414-417.
88. Wu, G.; Feng, X.; Stein, L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010, 11, R53.