Karin M, Greten FR. NF- κB: linking inflammation and immunity to cancer development and progression. Nat Rev Immunol. 2005; 5(10):749.
Article
CAS
PubMed
Google Scholar
Halazonetis TD, Gorgoulis VG, Bartek J. An oncogene-induced DNA damage model for cancer development. Science. 2008; 319(5868):1352–5.
Article
CAS
PubMed
Google Scholar
Derynck R, Akhurst RJ, Balmain A. TGF- β signaling in tumor suppression and cancer progression. Nat Genet. 2001; 29(2):117.
Article
CAS
PubMed
Google Scholar
Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, Karhu R, et al.Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res. 1997; 57(7):1222–7.
CAS
PubMed
Google Scholar
Zheng L, Wang L, Ajani J, Xie K. Molecular basis of gastric cancer development and progression. Gastric Cancer. 2004; 7(2):61–77.
Article
PubMed
Google Scholar
Iacobuzio-Donahue CA, Velculescu VE, Wolfgang CL, Hruban RH. Genetic basis of pancreas cancer development and progression: insights from whole-exome and whole-genome sequencing. In: AACR. Philadelphia: American Association for Cancer Research: 2012. http://clincancerres.aacrjournals.org/site/misc/about.xhtml.
Google Scholar
Symonds H, Krall L, Remington L, Saenz-Robles M, Lowe S, Jacks T, et al.p53-dependent apoptosis suppresses tumor growth and progression in vivo. Cell. 1994; 78(4):703–11.
Article
CAS
PubMed
Google Scholar
Vandin F, Raphael BJ, Upfal E. On the sample complexity of cancer pathways identification. J Comput Biol. 2016; 23(1):30–41. American Association for Cancer Research, Philadelphia.
Article
CAS
PubMed
PubMed Central
Google Scholar
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics. 2015; 31(12):i62–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013; 10(11):1108–15. http://dx.doi.org/10.1038/nmeth.2651.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leiserson MD, Vandin F, Wu HT, Dobson JR, Raphael BR. Pan-cancer identification of mutated pathways and protein complexes. In: AACR: 2014.
Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017; 18(9):551.
Article
CAS
PubMed
Google Scholar
Ruffalo M, Koyutürk M, Sharan R. Network-Based Integration of Disparate Omic Data To Identify “Silent Players” in Cancer. PLOS Comput Biol. 2015; 11(12):e1004595.
Article
PubMed
PubMed Central
CAS
Google Scholar
He Z, Zhang J, Yuan X, Liu Z, Liu B, Tuo S, et al.Network based stratification of major cancers by integrating somatic mutation and gene expression data. PloS ONE. 2017; 12(5):e0177662.
Article
PubMed
PubMed Central
CAS
Google Scholar
Patkar S, Magen A, Sharan R, Hannenhalli S. A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput Biol. 2017; 13(11):e1005793.
Article
PubMed
PubMed Central
CAS
Google Scholar
Thomas PJ, Qu BH, Pedersen PL. Defective protein folding as a basis of human disease. Trends Biochem Sci. 1995; 20(11):456–9.
Article
CAS
PubMed
Google Scholar
Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic acids research. 2005; 33(suppl_2):W306–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Moult J. SNPs, protein structure, and disease. Human Mutat. 2001; 17(4):263–70.
Article
Google Scholar
Minegishi Y, Saito M, Tsuchiya S, Tsuge I, Takada H, Hara T, et al.Dominant-negative mutations in the DNA-binding domain of STAT3 cause hyper-IgE syndrome. Nature. 2007; 448(7157):1058.
Article
CAS
PubMed
Google Scholar
Lee B, Thirunavukkarasu K, Zhou L, Pastore L, Baldini A, Hecht J, et al.Missense mutations abolishing DNA binding of the osteoblast-specific transcription factor OSF2/CBFA1 in cleidocranial dysplasia. Nat Genet. 1997; 16(3):307.
Article
CAS
PubMed
Google Scholar
Pavletich NP, Chambers KA, Pabo CO. The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots. Genes Dev. 1993; 7(12b):2556–64.
Article
CAS
PubMed
Google Scholar
Oitzl MS, Reichardt HM, Joëls M, de Kloet ER. Point mutation in the mouse glucocorticoid receptor preventing DNA binding impairs spatial memory. Proc Natl Acad Sci. 2001; 98(22):12790–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013; 339(6122):957–59. https://doi.org/10.1126/science.1229259.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, et al.Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 1997; 57(5):808–11.
CAS
PubMed
Google Scholar
Xing M, Liu R, Liu X, Murugan AK, Zhu G, Zeiger MA, et al.BRAF V600E and TERT promoter mutations cooperatively identify the most aggressive papillary thyroid cancer with highest recurrence. J Clin Oncol. 2014; 32(25):2718.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sarvagalla S, Cheung CHA, Tsai JY, Hsieh HP, Coumar MS. Disruption of protein–protein interactions: hot spot detection, structure-based virtual screening and in vitro testing for the anti-cancer drug target–survivin. Rsc Adv. 2016; 6(38):31947–59.
Article
CAS
Google Scholar
Petta I, Lievens S, Libert C, Tavernier J, De Bosscher K. Modulation of protein–protein interactions for the development of novel therapeutics. Mol Ther. 2016; 24(4):707–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Z, Ivanov AA, Su R, Gonzalez-Pecchi V, Qi Q, Liu S, et al.The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies. Nat Commun. 2017; 8:14356.
Article
CAS
PubMed
PubMed Central
Google Scholar
The Cancer Genome Atlas. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490(7418):61–70. http://dx.doi.org/10.1038/nature11412.
Article
CAS
Google Scholar
Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PLoS ONE. 2012; 7(2):e31826. https://doi.org/10.1371/journal.pone.0031826.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gitter A, Carmi M, Barkai N, Bar-Joseph Z. Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res. 2013; 23(2):365–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R. Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol. 2010; 6(1):e100641.
Article
CAS
Google Scholar
Kim P, Zhao J, Lu P, Zhao Z. mutLBSgeneDB: mutated ligand binding site gene DataBase. Nucleic Acids Res. 2016; 45(D1):D256–63.
Article
PubMed
PubMed Central
CAS
Google Scholar
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al.The Protein Data Bank. Nucleic Acids Res. 2000; 28(1):235–42. http://dx.doi.org/10.1093/nar/28.1.235.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schrödinger LLC. The PyMOL Molecular Graphics System, Version 1.8. 2015. https://pymol.org/2/. Accessed 21 Feb 2018.
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, et al.The ClusPro web server for protein–protein docking. Nat Protocol. 2017; 12(2):255.
Article
CAS
Google Scholar
Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, et al.Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005; 365(9460):671–9.
Article
CAS
PubMed
Google Scholar
Lunn M, McNeil D. Applying Cox regression to competing risks. Biometrics. 1995;:524–32.
Article
CAS
PubMed
Google Scholar
Järvelin K, Kekäläinen J. Cumulated gain-based evaluation of IR techniques. ACM Trans Inf Syst (TOIS). 2002; 20(4):422–46.
Article
Google Scholar
Burges C, Shaked T, Renshaw E, Lazier A, Deeds M, Hamilton N, et al.Learning to rank using gradient descent. In: Proceedings of the 22nd international conference on Machine learning. International Conference on Machine Learning. La Jolla: ACM: 2005. p. 89–96.
Google Scholar
West AC, Johnstone RW. New and emerging HDAC inhibitors for cancer treatment. J Clinic Investig. 2014; 124(1):30–9.
Article
CAS
Google Scholar
Chakrabarti A, Oehme I, Witt O, Oliveira G, Sippl W, Romier C, et al.HDAC8: a multifaceted target for therapeutic interventions. Trends Pharmacol Sci. 2015; 36(7):481–92.
Article
CAS
PubMed
Google Scholar
Petitjean A, Achatz M, Borresen-Dale A, Hainaut P, Olivier M. TP53 mutations in human cancers: functional selection and impact on cancer prognosis and outcomes. Oncogene. 2007; 26(15):2157.
Article
CAS
PubMed
Google Scholar
Olivier M, Langer A, Carrieri P, Bergh J, Klaar S, Eyfjord J, et al.The clinical value of somatic TP53 gene mutations in 1794 patients with breast cancer. Clinic Cancer Res. 2006; 12(4):1157–67.
Article
CAS
Google Scholar
Bougeard G, Limacher JM, Martin C, Charbonnier F, Killian A, Delattre O, et al.Detection of 11 germline inactivating TP53 mutations and absence of TP63 and HCHK2 mutations in 17 French families with Li-Fraumeni or Li-Fraumeni-like syndrome. J Med Genet. 2001; 38(4):253–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Papageorgis P, Ozturk S, Lambert AW, Neophytou CM, Tzatsos A, Wong CK, et al.Targeting IL13Ralpha2 activates STAT6-TP63 pathway to suppress breast cancer lung metastasis. Breast Cancer Res. 2015; 17(1):98.
Article
PubMed
PubMed Central
CAS
Google Scholar
Iscan M, Klaavuniemi T, Ċoban T, Kapucuoġlu N, Pelkonen O, Raunio H. The expression of cytochrome P450 enzymes in human breast tumours and normal breast tissue. Breast Cancer Res Treat. 2001; 70(1):47–54.
Article
CAS
PubMed
Google Scholar
Nakajima M, Itoh M, Sakai H, Fukami T, Katoh M, Yamazaki H, et al.CYP2A13 expressed in human bladder metabolically activates 4-aminobiphenyl. Int J Cancer. 2006; 119(11):2520–6.
Article
CAS
PubMed
Google Scholar
Maia CJ, Socorro S, Schmitt F, Santos CR. STEAP1 is over-expressed in breast cancer and down-regulated by 17 β-estradiol in MCF-7 cells and in the rat mammary gland. Endocrine. 2008; 34(1-3):108–16.
Article
CAS
PubMed
Google Scholar
Moreaux J, Kassambara A, Hose D, Klein B. STEAP1 is overexpressed in cancers: a promising therapeutic target. Biochem Biophys Res Commun. 2012; 429(3):148–55.
Article
CAS
PubMed
Google Scholar
Gomes IM, Arinto P, Lopes C, Santos CR, Maia CJ. STEAP1 is overexpressed in prostate cancer and prostatic intraepithelial neoplasia lesions, and it is positively associated with Gleason score. In: Urologic Oncology: Seminars and Original Investigations. Amsterdam: Elsevier: 2014. p. 53–e23.
Google Scholar
Kurotani R, Kumaki N, Naizhen X, Ward JM, Linnoila RI, Kimura S. Secretoglobin 3A2/uteroglobin-related protein 1 is a novel marker for pulmonary carcinoma in mice and humans. Lung Cancer. 2011; 71(1):42–8.
Article
PubMed
Google Scholar
La Fleur L, Boura VF, Alexeyenko A, Berglund A, Pontén V, Mattsson JS, et al.Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer. Int J Cancer. 2018; 143(7):1741–52.
Article
CAS
PubMed
Google Scholar
Espinosa O, Mitsopoulos K, Hakas J, Pearl F, Zvelebil M. Deriving a mutation index of carcinogenicity using protein structure and protein interfaces. PloS one. 2014; 9(1):e84598.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gauthier NP, Reznik E, Gao J, Sumer SO, Schultz N, Sander C, et al.MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. Nucleic Acids Res. 2015; 44(D1):D986–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Siderius M, Jagodzinski F. Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach. J Comput Biol. 2018; 25(1):89–102.
Article
CAS
PubMed
Google Scholar
Gomes IM, Santos CR, Maia CJ. Expression of STEAP1 and STEAP1B in prostate cell lines, and the putative regulation of STEAP1 by post-transcriptional and post-translational mechanisms. Genes Cancer. 2014; 5(3-4):142.
PubMed
PubMed Central
Google Scholar
Havrysh K, Kiyamova R. 14New potential biomarkers for breast cancer prognosis. Ann Oncol. 2017; 28(suppl7):mdx508.011. http://dx.doi.org/10.1093/annonc/mdx508.011.
Google Scholar
Kazerounian S, Pitari GM, Shah FJ, Frick GS, Madesh M, Ruiz-Stewart I, et al.Proliferative signaling by store-operated calcium channels opposes colon cancer cell cytostasis induced by bacterial enterotoxins. J Pharmacol Exp Ther. 2005; 314(3):1013–22.
Article
CAS
PubMed
Google Scholar
Luchino J, Hocine M, Amoureux MC, Gibert B, Bernet A, Royet A, et al.Semaphorin 3E suppresses tumor cell death triggered by the plexin D1 dependence receptor in metastatic breast cancers. Cancer Cell. 2013; 24(5):673–85.
Article
CAS
PubMed
Google Scholar
Kim SJ, Kim JS, Park ES, Lee JS, Lin Q, Langley RR, et al.Astrocytes upregulate survival genes in tumor cells and induce protection from chemotherapy. Neoplasia. 2011; 13(3):286–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liang D, Meyer L, Chang DW, Lin J, Pu X, Ye Y, et al.Genetic variants in MicroRNA biosynthesis pathways and binding sites modify ovarian cancer risk, survival, and treatment response. Cancer Res. 2010; 70(23):9765–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wegman P, Elingarami S, Carstensen J, Stål O, Nordenskjöld B, Wingren S. Genetic variants of CYP3A5, CYP2D6, SULT1A1, UGT2B15 and tamoxifen response in postmenopausal patients with breast cancer. Breast Cancer Res. 2007; 9(1):R7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shulby SA, Dolloff NG, Stearns ME, Meucci O, Fatatis A. CX3CR1-fractalkine expression regulates cellular mechanisms involved in adhesion, migration, and survival of human prostate cancer cells. Cancer Res. 2004; 64(14):4693–8.
Article
CAS
PubMed
Google Scholar
Andre F, Cabioglu N, Assi H, Sabourin J, Delaloge S, Sahin A, et al.Expression of chemokine receptors predicts the site of metastatic relapse in patients with axillary node positive primary breast cancer. Ann Oncol. 2006; 17(6):945–51.
Article
CAS
PubMed
Google Scholar
Tardáguila M, Mira E, García-Cabezas MA, Feijoo AM, Quintela-Fandino M, Azcoitia I, et al.CX3CL1 promotes breast cancer via transactivation of the EGF pathway. Cancer Res. 2013; 73(14):4461–73.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cui J, Li F, Wang G, Fang X, Puett JD, Xu Y. Gene-expression signatures can distinguish gastric cancer grades and stages. PloS one. 2011; 6(3):e17819.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao C, Cheng X, Li X, Tong B, Wu K, Liu Y. Prognostic significance of artemin and GFR α1 expression in laryngeal squamous cell carcinoma. Exp Ther Med. 2014; 8(3):818–22. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113528/. Etm-08-03-0818[PII].
Article
PubMed
PubMed Central
Google Scholar
Ito Y, Okada Y, Sato M, Sawai H, Funahashi H, Murase T, et al.Expression of glial cell line–derived neurotrophic factor family members and their receptors in pancreatic cancers. Surgery. 2005; 138(4):788–94.
Article
PubMed
Google Scholar
Pandey V, Qian PX, Kang J, Perry JK, Mitchell MD, Yin Z, et al.Artemin stimulates oncogenicity and invasiveness of human endometrial carcinoma cells. Endocrinology. 2010; 151(3):909–20.
Article
CAS
PubMed
Google Scholar
Ngollo M, Lebert A, Daures M, Judes G, Rifai K, Dubois L, et al.Global analysis of H3K27me3 as an epigenetic marker in prostate cancer progression. BMC cancer. 2017; 17(1):261.
Article
PubMed
PubMed Central
CAS
Google Scholar
Saito T, Kasamatsu A, Ogawara K, Miyamoto I, Saito K, Iyoda M, et al.Semaphorin7A promotion of tumoral growth and metastasis in human oral cancer by regulation of G1 cell cycle and matrix metalloproteases: Possible contribution to tumoral angiogenesis. PloS one. 2015; 10(9):e0137923.
Article
PubMed
PubMed Central
CAS
Google Scholar
Udabage L, Brownlee GR, Nilsson SK, Brown TJ. The over-expression of HAS2, Hyal-2 and CD44 is implicated in the invasiveness of breast cancer. Exp Cell Res. 2005; 310(1):205–17.
Article
CAS
PubMed
Google Scholar
Liu N, Gao F, Han Z, Xu X, Underhill CB, Zhang L. Hyaluronan synthase 3 overexpression promotes the growth of TSU prostate cancer cells. Cancer Res. 2001; 61(13):5207–14.
CAS
PubMed
Google Scholar
Alves IT, Hartjes T, McClellan E, Hiltemann S, Böttcher R, Dits N, et al.Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer. Oncogene. 2015; 34(5):568.
Article
CAS
Google Scholar
Guo JC, Li CQ, Wang QY, Zhao JM, Ding JY, Li EM, et al.Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature. Mol BioSyst. 2016; 12(11):3467–77.
Article
CAS
PubMed
Google Scholar
Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, et al.Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ER α- breast cancer. Proc Natl Acad Sci. 2012; 109(15):5832–7. http://www.pnas.org/content/109/15/5832.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marcucci G, Maharry K, Wu YZ, Radmacher MD, Mrózek K, Margeson D, et al.IDH1 and IDH2 gene mutations identify novel molecular subsets within de novo cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clinic Oncol. 2010; 28(14):2348.
Article
CAS
Google Scholar
Jutras S, Bachvarova M, Keita M, Bascands JL, Mes-Masson AM, Stewart JM, et al.Strong cytotoxic effect of the bradykinin antagonist BKM-570 in ovarian cancer cells–analysis of the molecular mechanisms of its antiproliferative action. FEBS J. 2010; 277(24):5146–60.
Article
CAS
PubMed
Google Scholar
L’Espérance S, Bachvarova M, Tetu B, Mes-Masson AM, Bachvarov D. Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids. BMC Genomics. 2008; 9(1):99.
Article
PubMed
PubMed Central
CAS
Google Scholar
Baba T, Sakamoto Y, Kasamatsu A, Minakawa Y, Yokota S, Higo M, et al.Persephin: A potential key component in human oral cancer progression through the RET receptor tyrosine kinase-mitogen-activated protein kinase signaling pathway. Mol Carcinog. 2015; 54(8):608–17.
Article
CAS
PubMed
Google Scholar
Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, et al.Proteome-wide discovery of mislocated proteins in cancer. Genome Res. 2013; 23(8):1283–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thompson MP, Cooper ST, Parry BR, Tuckey JA. Increased expression of the mRNA for hormone-sensitive lipase in adipose tissue of cancer patients. Biochim Biophys Acta (BBA)-Mol Basis Dis. 1993; 1180(3):236–42.
Article
CAS
Google Scholar
Nath A, Chan C. Genetic alterations in fatty acid transport and metabolism genes are associated with metastatic progression and poor prognosis of human cancers. Sci Rep. 2016; 6:18669.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D, et al.Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 2012; 22(2):271–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin PC, Giannopoulou EG, Park K, Mosquera JM, Sboner A, Tewari AK, et al.Epigenomic alterations in localized and advanced prostate cancer. Neoplasia. 2013; 15(4):IN2–5.
Article
CAS
Google Scholar