Muller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, et al: Regulatory networks define phenotypic classes of human stem cell lines. Nature. 2008, 455 (7211): 401-405. 10.1038/nature07213.
Article
PubMed
PubMed Central
Google Scholar
Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D, Bilbe G: Applications of a rat multiple tissue gene expression data set. Genome Res. 2004, 14 (4): 742-749. 10.1101/gr.2161804.
Article
PubMed
CAS
PubMed Central
Google Scholar
Magwene PM, Kim J: Estimating genomic coexpression networks using first-order conditional independence. Genome Biol. 2004, 5 (12): R100-10.1186/gb-2004-5-12-r100.
Article
PubMed
PubMed Central
Google Scholar
Kar G, Gursoy A, Keskin O: Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol. 2009, 5 (12): e1000601-10.1371/journal.pcbi.1000601.
Article
PubMed
PubMed Central
Google Scholar
Hanahan D, Weinberg RA: The hallmarks of cancer. Cell. 2000, 100 (1): 57-70. 10.1016/S0092-8674(00)81683-9.
Article
PubMed
CAS
Google Scholar
Wong DJ, Segal E, Chang HY: Stemness, cancer and cancer stem cells. Cell Cycle. 2008, 7 (23): 3622-3624. 10.4161/cc.7.23.7104.
Article
PubMed
CAS
Google Scholar
Glinsky GV: “Stemness” genomics law governs clinical behavior of human cancer: implications for decision making in disease management. J Clin Oncol. 2008, 26 (17): 2846-2853. 10.1200/JCO.2008.17.0266.
Article
PubMed
Google Scholar
Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell. 2011, 144 (5): 646-674. 10.1016/j.cell.2011.02.013.
Article
PubMed
CAS
Google Scholar
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM: NCBI GEO, et al: archive for functional genomics data sets--10 years on. Nucleic Acids Res. 2011, 39 (Database issue): D1005-D1010.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, et al: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006, 439 (7074): 353-357. 10.1038/nature04296.
Article
PubMed
CAS
Google Scholar
Zhang W, Laborde PM, Coombes KR, Berry DA, Hamilton SR: Cancer genomics: promises and complexities. Clin Cancer Res. 2001, 7 (8): 2159-2167.
PubMed
CAS
Google Scholar
Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP: Sparse combinatorial inference with an application in cancer biology. Bioinformatics. 2009, 25 (2): 265-271. 10.1093/bioinformatics/btn611.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kooperberg C, Ruczinski I: Identifying interacting SNPs using Monte Carlo logic regression. Genet Epidemiol. 2005, 28 (2): 157-170. 10.1002/gepi.20042.
Article
PubMed
Google Scholar
Schwender H, Ruczinski I: Logic regression and its extensions. Adv Genet. 2010, 72: 25-45.
Article
PubMed
Google Scholar
Nagaraj SH, Reverter A: A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer. BMC Syst Biol. 2011, 5: 35-10.1186/1752-0509-5-35.
Article
PubMed
PubMed Central
Google Scholar
Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH: Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet. 2001, 69 (1): 138-147. 10.1086/321276.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cancer Genome Atlas Research Network: Integrated genomic analyses of ovarian carcinoma. Nature. 2011, 474 (7353): 609-615. 10.1038/nature10166.
Article
Google Scholar
Breitling R, Armengaud P, Amtmann A, Herzyk P: Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 2004, 573 (1–3): 83-92.
Article
PubMed
CAS
Google Scholar
Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S: A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci USA. 2008, 105 (52): 20870-20875. 10.1073/pnas.0810772105.
Article
PubMed
CAS
PubMed Central
Google Scholar
Latchman DS: Transcription-factor mutations and disease. N Engl J Med. 1996, 334 (1): 28-33. 10.1056/NEJM199601043340108.
Article
PubMed
CAS
Google Scholar
Seth A, Watson DK: ETS transcription factors and their emerging roles in human cancer. Eur J Cancer. 2005, 41 (16): 2462-2478. 10.1016/j.ejca.2005.08.013.
Article
PubMed
CAS
Google Scholar
Dahlman-Wright K, Qiao Y, Jonsson P, Gustafsson JA, Williams C, Zhao C: Interplay between AP-1 and estrogen receptor alpha in regulating gene expression and proliferation networks in breast cancer cells. Carcinogenesis. 2012, 33 (9): 1684-1691. 10.1093/carcin/bgs223.
Article
PubMed
CAS
Google Scholar
Krueger KE, Srivastava S: Posttranslational protein modifications: current implications for cancer detection, prevention, and therapeutics. Mol Cell Proteomics. 2006, 5 (10): 1799-1810. 10.1074/mcp.R600009-MCP200.
Article
PubMed
CAS
Google Scholar
Anbalagan M, Huderson B, Murphy L, Rowan BG: Post-translational modifications of nuclear receptors and human disease. Nucl Recept Signal. 2012, 10: e001-
PubMed
CAS
PubMed Central
Google Scholar
Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, 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 (Database issue): D945-D950.
Article
PubMed
CAS
PubMed Central
Google Scholar
Callesen AK, Mogensen O, Jensen AK, Kruse TA, Martinussen T, Jensen ON, Madsen JS: Reproducibility of mass spectrometry based protein profiles for diagnosis of ovarian cancer across clinical studies: A systematic review. J Proteomics. 2012, 75 (10): 2758-2772. 10.1016/j.jprot.2012.02.007.
Article
PubMed
CAS
Google Scholar
Mok SC, Chao J, Skates S, Wong K, Yiu GK, Muto MG, Berkowitz RS, Cramer DW: Prostasin, a potential serum marker for ovarian cancer: identification through microarray technology. J Natl Cancer Inst. 2001, 93 (19): 1458-1464. 10.1093/jnci/93.19.1458.
Article
PubMed
CAS
Google Scholar
Kim JH, Skates SJ, Uede T, Wong KK, Schorge JO, Feltmate CM, Berkowitz RS, Cramer DW, Mok SC: Osteopontin as a potential diagnostic biomarker for ovarian cancer. JAMA. 2002, 287 (13): 1671-1679. 10.1001/jama.287.13.1671.
Article
PubMed
CAS
Google Scholar
Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin CH, Smoot M, Sahasrabudhe S, et al: A human MAP kinase interactome. Nat Methods. 2010, 7 (10): 801-805. 10.1038/nmeth.1506.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hatada I, Fukasawa M, Kimura M, Morita S, Yamada K, Yoshikawa T, Yamanaka S, Endo C, Sakurada A, Sato M, et al: Genome-wide profiling of promoter methylation in human. Oncogene. 2006, 25 (21): 3059-3064. 10.1038/sj.onc.1209331.
Article
PubMed
CAS
Google Scholar
Huret JL, Dessen P, Bernheim A: Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003. Nucleic Acids Res. 2003, 31 (1): 272-274. 10.1093/nar/gkg126.
Article
PubMed
CAS
PubMed Central
Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer. 2004, 4 (3): 177-183. 10.1038/nrc1299.
Article
PubMed
CAS
PubMed Central
Google Scholar
Prasad TS, Kandasamy K, Pandey A: Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol. 2009, 577: 67-79. 10.1007/978-1-60761-232-2_6.
Article
PubMed
CAS
Google Scholar
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The protein kinase complement of the human genome. Science. 2002, 298 (5600): 1912-1934. 10.1126/science.1075762.
Article
PubMed
CAS
Google Scholar
Jiang C, Xuan Z, Zhao F, Zhang MQ: TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 2007, 35 (Database issue): D137-D140.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen YA, Tripathi LP, Mizuguchi K: TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PLoS One. 2011, 6 (3): e17844-10.1371/journal.pone.0017844.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mankoo PK, Shen R, Schultz N, Levine DA, Sander C: Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. PLoS One. 2011, 6 (11): e24709-10.1371/journal.pone.0024709.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gilbert D: Biomolecular interaction network database. Brief Bioinform. 2005, 6 (2): 194-198. 10.1093/bib/6.2.194.
Article
PubMed
CAS
Google Scholar
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, et al: The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39 (Database issue): D698-D704.
Article
PubMed
CAS
PubMed Central
Google Scholar
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, 32 (Database issue): D449-D451.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, et al: IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2007, 35 (Database issue): D561-D565.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G: MINT, the molecular interaction database: 2009 update. Nucleic Acids Res. 2010, 38 (Database issue): D532-D539.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stein A, Ceol A, Aloy P: 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2011, 39 (Database issue): D718-D723.
Article
PubMed
CAS
PubMed Central
Google Scholar
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al: The Pfam protein families database. Nucleic Acids Res. 2010, 38 (Database issue): D211-D222.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al: The HUPO PSI’s molecular interaction format–a community standard for the representation of protein interaction data. Nat Biotechnol. 2004, 22 (2): 177-183. 10.1038/nbt926.
Article
PubMed
CAS
Google Scholar
Patil A, Nakai K, Kinoshita K: Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks. BMC Genomics. 2011, 12 (Suppl 3): S19-10.1186/1471-2164-12-S3-S19.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen R, Li L, Butte AJ: AILUN: reannotating gene expression data automatically. Nat Methods. 2007, 4 (11): 879-10.1038/nmeth1107-879.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O’Connor-McCourt M, et al: A map of human cancer signaling. Mol Syst Biol. 2007, 3: 152-
Article
PubMed
PubMed Central
Google Scholar
Csardi G, Nepusz T: The igraph software package for complex network research. InterJ Complex Syst. 2006, 1695-http://igraph.sf.net 2013 Feb 4
Google Scholar
Papanikolaou V, Iliopoulos D, Dimou I, Dubos S, Kappas C, Kitsiou-Tzeli S, Tsezou A: Survivin regulation by HER2 through NF-kappaB and c-myc in irradiated breast cancer cells. J Cell Mol Med. 2011, 15 (7): 1542-1550. 10.1111/j.1582-4934.2010.01149.x.
Article
PubMed
CAS
PubMed Central
Google Scholar
Shiratsuchi I, Akagi Y, Kawahara A, Kinugasa T, Romeo K, Yoshida T, Ryu Y, Gotanda Y, Kage M, Shirouzu K: Expression of IGF-1 and IGF-1R and their relation to clinicopathological factors in colorectal cancer. Anticancer Res. 2011, 31 (7): 2541-2545.
PubMed
CAS
Google Scholar
Mejia W, Castro C, Umana A, de Castro C, Riveros T, Sanchez-Gomez M: [Insulin-like growth factor receptor I signaling in a breast cancer cell line]. Biomedica. 2010, 30 (4): 551-558.
Article
PubMed
Google Scholar
Jia SH, Parodo J, Kapus A, Rotstein OD, Marshall JC: Dynamic regulation of neutrophil survival through tyrosine phosphorylation or dephosphorylation of caspase-8. J Biol Chem. 2008, 283 (9): 5402-5413.
Article
PubMed
CAS
Google Scholar
Kulkarni AA, Kingsbury SR, Tudzarova S, Hong HK, Loddo M, Rashid M, Rodriguez-Acebes S, Prevost AT, Ledermann JA, Stoeber K, et al: Cdc7 kinase is a predictor of survival and a novel therapeutic target in epithelial ovarian carcinoma. Clin Cancer Res. 2009, 15 (7): 2417-2425. 10.1158/1078-0432.CCR-08-1276.
Article
PubMed
CAS
Google Scholar
Ricke RM, Jeganathan KB, van Deursen JM: Bub1 overexpression induces aneuploidy and tumor formation through Aurora B kinase hyperactivation. J Cell Biol. 2011, 193 (6): 1049-1064. 10.1083/jcb.201012035.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thorsen K, Schepeler T, Oster B, Rasmussen MH, Vang S, Wang K, Hansen KQ, Lamy P, Pedersen JS, Eller A, et al: Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics. 2011, 12: 505-10.1186/1471-2164-12-505.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hoglund A, Nilsson LM, Muralidharan SV, Hasvold LA, Merta P, Rudelius M, Nikolova V, Keller U, Nilsson JA: Therapeutic implications for the induced levels of chk1 in myc-expressing cancer cells. Clin Cancer Res. 2011, 17 (22): 7067-7079. 10.1158/1078-0432.CCR-11-1198.
Article
PubMed
Google Scholar
Indra D, Mitra S, Singh RK, Dutta S, Roy A, Mondal RK, Basu PS, Roychoudhury S, Panda CK: Inactivation of CHEK1 and EI24 are associated with the development of invasive cervical carcinoma: Clinical and prognostic implications. Int J Cancer. 2011, 129 (8): 1859-1871. 10.1002/ijc.25849.
Article
Google Scholar
O’Mara TA, Ferguson K, Fahey P, Marquart L, Yang HP, Lissowska J, Chanock S, Garcia-Closas M, Thompson DJ, Healey CS, et al: CHEK2, MGMT, SULT1E1 and SULT1A1 polymorphisms and endometrial cancer risk. Twin Res Hum Genet. 2011, 14 (4): 328-332. 10.1375/twin.14.4.328.
Article
PubMed
PubMed Central
Google Scholar
Di Cera E: Serine proteases. IUBMB Life. 2009, 61 (5): 510-515. 10.1002/iub.186.
Article
PubMed
CAS
PubMed Central
Google Scholar
Page MJ, Di Cera E: Serine peptidases: classification, structure and function. Cell Mol Life Sci. 2008, 65 (7–8): 1220-1236.
Article
PubMed
CAS
Google Scholar
Rezze GG, Fregnani JH, Duprat J, Landman G: Cell adhesion and communication proteins are differentially expressed in melanoma progression model. Hum Pathol. 2011, 42 (3): 409-418. 10.1016/j.humpath.2010.09.004.
Article
PubMed
CAS
Google Scholar
Kim JT, Song EY, Chung KS, Kang MA, Kim JW, Kim SJ, Yeom YI, Kim JH, Kim KH, Lee HG: Up-regulation and clinical significance of serine protease kallikrein 6 in colon cancer. Cancer. 2011, 117 (12): 2608-2619. 10.1002/cncr.25841.
Article
PubMed
CAS
Google Scholar
Law AY, Wong CK: Stanniocalcin-2 promotes epithelial-mesenchymal transition and invasiveness in hypoxic human ovarian cancer cells. Exp Cell Res. 2010, 316 (20): 3425-3434. 10.1016/j.yexcr.2010.06.026.
Article
PubMed
CAS
Google Scholar
Moretti RM, Mai S, Montagnani Marelli M, Rizzi F, Bettuzzi S, Limonta P: Molecular mechanisms of the antimetastatic activity of nuclear clusterin in prostate cancer cells. Int J Oncol. 2011, 39 (1): 225-234.
PubMed
CAS
Google Scholar
Miyamoto T, Asaka R, Suzuki A, Takatsu A, Kashima H, Shiozawa T: Immunohistochemical detection of a specific receptor for lipocalin2 (solute carrier family 22 member 17, SLC22A17) and its prognostic significance in endometrial carcinoma. Exp Mol Pathol. 2011, 91 (2): 563-568. 10.1016/j.yexmp.2011.06.002.
Article
PubMed
CAS
Google Scholar
Hannigan A, Smith P, Kalna G, Lo Nigro C, Orange C, O’Brien DI, Shah R, Syed N, Spender LC, Herrera B, et al: Epigenetic downregulation of human disabled homolog 2 switches TGF-beta from a tumor suppressor to a tumor promoter. J Clin Invest. 2010, 120 (8): 2842-2857. 10.1172/JCI36125.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen Y, Cui T, Knosel T, Yang L, Zoller K, Petersen I: IGFBP7 is a p53 target gene inactivated in human lung cancer by DNA hypermethylation. Lung Cancer. 2011, 73 (1): 38-44. 10.1016/j.lungcan.2010.10.015.
Article
PubMed
Google Scholar
Sharma NL, Massie CE, Ramos-Montoya A, Zecchini V, Scott HE, Lamb AD, Macarthur S, Stark R, Warren AY, Mills IG, et al: The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man. Cancer Cell. 2012
Google Scholar
Lau KM, Mok SC, Ho SM: Expression of human estrogen receptor-alpha and -beta, progesterone receptor, and androgen receptor mRNA in normal and malignant ovarian epithelial cells. Proc Natl Acad Sci USA. 1999, 96 (10): 5722-5727. 10.1073/pnas.96.10.5722.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chang JT, Nevins JR: GATHER: a systems approach to interpreting genomics signatures. Bioinformatics. 2006, 22 (23): 2926-33. 10.1093/bioinformatics/btl483.
Article
PubMed
CAS
Google Scholar
Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M, Lancet D: In-silico human genomics with GeneCards. Hum Genomics. 2011, 5 (6): 709-17.
Article
PubMed
CAS
PubMed Central
Google Scholar
Liekens AM, De Knijf J, Daelemans W, Goethals B, De Rijk P, Del-Favero J: BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. Genome Biol. 2011, 12 (6): R57-10.1186/gb-2011-12-6-r57.
Article
PubMed
PubMed Central
Google Scholar
Dai Y, Grant S: New insights into checkpoint kinase 1 in the DNA damage response signaling network. Clin Cancer Res. 2010, 16 (2): 376-383. 10.1158/1078-0432.CCR-09-1029.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nodin B, Zendehrokh N, Brändstedt J, Nilsson E, Manjer J, Brennan DJ, Jirström K: Increased androgen receptor expression in serous carcinoma of the ovary is associated with an improved survival. J Ovarian Res. 2010, 3: 14-10.1186/1757-2215-3-14.
Article
PubMed
PubMed Central
Google Scholar
Zhang S, Liu CC, Li W, Shen H, Laird PW, Zhou XJ: Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res. 2012, 40 (19): 9379-9391. 10.1093/nar/gks725.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li J, Lenferink AE, Deng Y, Collins C, Cui Q, Purisima EO, O’Connor-McCourt MD, Wang E: Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun. 2010, 1: 34-
PubMed
Google Scholar