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Volumn 8, Issue 1, 2018, Pages

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with slapenrich

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DISSECTION; DRIVER; HUMAN; MAJOR CLINICAL STUDY; SOMATIC MUTATION; STATISTICS; TUMOR GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GENOMICS; HUMAN GENOME; MUTATION; NEOPLASM; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

EID: 85046621112     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-25076-6     Document Type: Article
Times cited : (19)

References (73)
  • 1
    • 84884994218 scopus 로고    scopus 로고
    • The cancer genome atlas pan-cancer analysis project
    • Weinstein, J. N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nature genetics 45, 1113-1120 (2013).
    • (2013) Nature Genetics , vol.45 , pp. 1113-1120
    • Weinstein, J.N.1
  • 3
    • 84859187259 scopus 로고    scopus 로고
    • Systematic identification of genomic markers of drug sensitivity in cancer cells
    • Garnett, M. J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570-575 (2012).
    • (2012) Nature , vol.483 , pp. 570-575
    • Garnett, M.J.1
  • 4
    • 84859169877 scopus 로고    scopus 로고
    • The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
    • Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
    • (2012) Nature , vol.483 , pp. 603-607
    • Barretina, J.1
  • 5
    • 84892833777 scopus 로고    scopus 로고
    • Discovery and saturation analysis of cancer genes across 21 tumour types
    • Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014).
    • (2014) Nature , vol.505 , pp. 495-501
    • Lawrence, M.S.1
  • 6
    • 84875758730 scopus 로고    scopus 로고
    • Lessons from the cancer genome
    • Garraway, L. A. & Lander, E. S. Lessons from the Cancer Genome. Cell 153, 17-37 (2013).
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 8
    • 79952635505 scopus 로고    scopus 로고
    • Principles and strategies for developing network models in cancer
    • Pe'er, D. & Hacohen, N. Principles and strategies for developing network models in cancer. Cell 144, 864-873 (2011).
    • (2011) Cell , vol.144 , pp. 864-873
    • Pe'Er, D.1    Hacohen, N.2
  • 9
    • 85016442123 scopus 로고    scopus 로고
    • Pathway level alterations rather than mutations in single genes predict response to HER2-Targeted therapies in the neo-Altto trial
    • Shi, W. et al. Pathway level alterations rather than mutations in single genes predict response to HER2-Targeted therapies in the neo-ALTTO trial. Annals of Oncology mdw434 (2016).
    • (2016) Annals of Oncology mdw434
    • Shi, W.1
  • 11
    • 84926157747 scopus 로고    scopus 로고
    • Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
    • Leiserson, M. D. M. et al. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature genetics 47, 106-114 (2015).
    • (2015) Nature Genetics , vol.47 , pp. 106-114
    • Leiserson, M.D.M.1
  • 12
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: The next generation. Cell 144, 646-674 (2011).
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 13
    • 84875490185 scopus 로고    scopus 로고
    • Cancer genome landscapes
    • Vogelstein, B. et al. Cancer Genome Landscapes. Science (New York, NY) 339, 1546-1558 (2013).
    • (2013) Science (New York, NY) , vol.339 , pp. 1546-1558
    • Vogelstein, B.1
  • 14
    • 79958127503 scopus 로고    scopus 로고
    • PathScan: A tool for discerning mutational significance in groups of putative cancer genes
    • Wendl, M. C. et al. PathScan: A tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics 27, 1595-1602 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1595-1602
    • Wendl, M.C.1
  • 16
    • 84934268985 scopus 로고    scopus 로고
    • Pathway and network analysis of cancer genomes
    • Creixell, P. et al. Pathway and network analysis of cancer genomes. Nature Methods 12, 615-621 (2015).
    • (2015) Nature Methods , vol.12 , pp. 615-621
    • Creixell, P.1
  • 17
    • 79959923522 scopus 로고    scopus 로고
    • G:Profiler-A web server for functional interpretation of gene lists (2011 update)
    • Reimand, J., Arak, T. & Vilo, J. g:Profiler-A web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research 39, W307-W315 (2011).
    • (2011) Nucleic Acids Research , vol.39 , pp. W307-W315
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 18
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., Navon, R., Steinfeld, I., Lipson, D. & Yakhini, Z. GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC bioinformatics 10, 48 (2009).
    • (2009) BMC Bioinformatics , vol.10
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 19
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44-57 (2008).
    • (2008) Nature Protocols , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 20
    • 84866911829 scopus 로고    scopus 로고
    • Camera: A competitive gene set test accounting for inter-gene correlation
    • Wu, D. & Smyth, G. K. Camera: A competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133-e133 (2012).
    • (2012) Nucleic Acids Research , vol.40 , pp. e133-e133
    • Wu, D.1    Smyth, G.K.2
  • 22
    • 84856535081 scopus 로고    scopus 로고
    • Mutual exclusivity analysis identifies oncogenic network modules
    • Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Research 22, 398-406 (2012).
    • (2012) Genome Research , vol.22 , pp. 398-406
    • Ciriello, G.1    Cerami, E.2    Sander, C.3    Schultz, N.4
  • 23
    • 84856532705 scopus 로고    scopus 로고
    • De novo discovery of mutated driver pathways in cancer
    • Vandin, F., Upfal, E. & Raphael, B. J. De novo discovery of mutated driver pathways in cancer. Genome Research 22, 375-385 (2012).
    • (2012) Genome Research , vol.22 , pp. 375-385
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 24
    • 84919787552 scopus 로고    scopus 로고
    • Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery
    • Schubert, M. & Iorio, F. Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery. Pharmacogenomics 15, 1943-1946 (2014).
    • (2014) Pharmacogenomics , vol.15 , pp. 1943-1946
    • Schubert, M.1    Iorio, F.2
  • 25
    • 84969730516 scopus 로고    scopus 로고
    • Identification of driver pathways in cancer based on combinatorial patterns of somatic gene mutations
    • Li, H. T., Zhang, J., Xia, J. & Zheng, C. H. Identification of driver pathways in cancer based on combinatorial patterns of somatic gene mutations. Neoplasma 63, 57-63 (2016).
    • (2016) Neoplasma , vol.63 , pp. 57-63
    • Li, H.T.1    Zhang, J.2    Xia, J.3    Zheng, C.H.4
  • 26
    • 84940755892 scopus 로고    scopus 로고
    • Identifying driver genomic alterations in cancers by searching minimum-Weight, mutually exclusive sets
    • Lu, S. et al. Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PLoS computational biology 11, e1004257 (2015).
    • (2015) PLoS Computational Biology , vol.11 , pp. e1004257
    • Lu, S.1
  • 28
    • 48749118242 scopus 로고    scopus 로고
    • Combinatorial patterns of somatic gene mutations in cancer
    • Yeang, C. H., McCormick, F. & Levine, A. Combinatorial patterns of somatic gene mutations in cancer. The FASEB Journal 22, 2605-2622 (2008).
    • (2008) The FASEB Journal , vol.22 , pp. 2605-2622
    • Yeang, C.H.1    McCormick, F.2    Levine, A.3
  • 29
    • 78651439545 scopus 로고    scopus 로고
    • Identifying cancer driver genes in tumor genome sequencing studies
    • Youn, A. & Simon, R. Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics 27, 175-181 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 175-181
    • Youn, A.1    Simon, R.2
  • 30
    • 33847293670 scopus 로고    scopus 로고
    • High-Throughput oncogene mutation profiling in human cancer
    • Thomas, R. K. et al. High-Throughput oncogene mutation profiling in human cancer. Nature genetics 39, 347-351 (2007).
    • (2007) Nature Genetics , vol.39 , pp. 347-351
    • Thomas, R.K.1
  • 33
    • 78651332286 scopus 로고    scopus 로고
    • Pathway Commons, a web resource for biological pathway data
    • Cerami, E. G. et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Research 39, D685-90 (2011).
    • (2011) Nucleic Acids Research , vol.39 , pp. D685-D690
    • Cerami, E.G.1
  • 34
    • 84979649916 scopus 로고    scopus 로고
    • A landscape of pharmacogenomic interactions in cancer
    • Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell (2016).
    • (2016) Cell
    • Iorio, F.1
  • 36
    • 84924279179 scopus 로고    scopus 로고
    • In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities
    • Rubio-Perez, C. et al. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell 27, 382-396 (2015).
    • (2015) Cancer Cell , vol.27 , pp. 382-396
    • Rubio-Perez, C.1
  • 37
    • 84954381684 scopus 로고    scopus 로고
    • Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas
    • Manié, E. et al. Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. International Journal of Cancer 138, 891-900 (2016).
    • (2016) International Journal of Cancer , vol.138 , pp. 891-900
    • Manié, E.1
  • 38
    • 84933279541 scopus 로고    scopus 로고
    • Two decades beyond BRCA1/2: Homologous recombination, hereditary cancer risk and a target for ovarian cancer therapy
    • Walsh, C. S. Two decades beyond BRCA1/2: Homologous recombination, hereditary cancer risk and a target for ovarian cancer therapy. Gynecologic oncology 137, 343-350 (2015).
    • (2015) Gynecologic Oncology , vol.137 , pp. 343-350
    • Walsh, C.S.1
  • 41
    • 84882837534 scopus 로고    scopus 로고
    • Signatures of mutational processes in human cancer
    • Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
    • (2013) Nature , vol.500 , pp. 415-421
    • Alexandrov, L.B.1
  • 43
    • 79951500251 scopus 로고    scopus 로고
    • The ATM kinase induces microRNA biogenesis in the DNA damage response
    • Zhang, X., Wan, G., Berger, F. G., He, X. & Lu, X. The ATM kinase induces microRNA biogenesis in the DNA damage response. Molecular cell 41, 371-383 (2011).
    • (2011) Molecular Cell , vol.41 , pp. 371-383
    • Zhang, X.1    Wan, G.2    Berger, F.G.3    He, X.4    Lu, X.5
  • 44
    • 84929481480 scopus 로고    scopus 로고
    • Pembrolizumab for the treatment of non-small-cell lung cancer
    • Garon, E. B. et al. Pembrolizumab for the treatment of non-small-cell lung cancer. The New England journal of medicine 372, 2018-2028 (2015).
    • (2015) The New England Journal of Medicine , vol.372 , pp. 2018-2028
    • Garon, E.B.1
  • 45
    • 84929481481 scopus 로고    scopus 로고
    • Pembrolizumab versus Ipilimumab in Advanced Melanoma
    • Robert, C. et al. Pembrolizumab versus Ipilimumab in Advanced Melanoma. The New England journal of medicine 372, 2521-2532 (2015).
    • (2015) The New England Journal of Medicine , vol.372 , pp. 2521-2532
    • Robert, C.1
  • 46
    • 84946607195 scopus 로고    scopus 로고
    • Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma
    • Motzer, R. J. et al. Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma. The New England journal of medicine 373, 1803-1813 (2015).
    • (2015) The New England Journal of Medicine , vol.373 , pp. 1803-1813
    • Motzer, R.J.1
  • 47
    • 84932628341 scopus 로고    scopus 로고
    • PD-1 blockade in tumors with mismatch-repair deficiency
    • Le, D. T. et al. PD-1 Blockade in Tumors with Mismatch-Repair Deficiency. The New England journal of medicine 372, 2509-2520 (2015).
    • (2015) The New England Journal of Medicine , vol.372 , pp. 2509-2520
    • Le, D.T.1
  • 50
    • 84962419838 scopus 로고    scopus 로고
    • Inflammatory networks underlying colorectal cancer
    • Lasry, A., Zinger, A. & Ben-Neriah, Y. Inflammatory networks underlying colorectal cancer. Nature immunology 17, 230-240 (2016).
    • (2016) Nature Immunology , vol.17 , pp. 230-240
    • Lasry, A.1    Zinger, A.2    Ben-Neriah, Y.3
  • 51
    • 84876004187 scopus 로고    scopus 로고
    • Reversing the Warburg effect as a treatment for glioblastoma
    • Poteet, E. et al. Reversing the Warburg effect as a treatment for glioblastoma. Journal of Biological Chemistry 288, 9153-9164 (2013).
    • (2013) Journal of Biological Chemistry , vol.288 , pp. 9153-9164
    • Poteet, E.1
  • 52
    • 84890312233 scopus 로고    scopus 로고
    • The detection and implication of genome instability in cancer
    • Pikor, L., Thu, K., Vucic, E. & Lam, W. The detection and implication of genome instability in cancer. Cancer metastasis reviews 32, 341-352 (2013).
    • (2013) Cancer Metastasis Reviews , vol.32 , pp. 341-352
    • Pikor, L.1    Thu, K.2    Vucic, E.3    Lam, W.4
  • 53
    • 77950346282 scopus 로고    scopus 로고
    • Immunity, inflammation, and cancer
    • Grivennikov, S. I., Greten, F. R. & Karin, M. Immunity, inflammation, and cancer. Cell 140, 883-899 (2010).
    • (2010) Cell , vol.140 , pp. 883-899
    • Grivennikov, S.I.1    Greten, F.R.2    Karin, M.3
  • 55
    • 0034996039 scopus 로고    scopus 로고
    • The role of the plasminogen activation system in angiogenesis and metastasis
    • Rabbani, S. A. & Mazar, A. P. The role of the plasminogen activation system in angiogenesis and metastasis. Surgical oncology clinics of North America 10, 393-415 (2001).
    • (2001) Surgical Oncology Clinics of North America , vol.10 , pp. 393-415
    • Rabbani, S.A.1    Mazar, A.P.2
  • 56
    • 84982789818 scopus 로고    scopus 로고
    • New Insight on the role of plasminogen receptor in cancer progression
    • Kumari, S. & Malla, R. New Insight on the Role of Plasminogen Receptor in Cancer Progression. Cancer growth and metastasis 8, 35-42 (2015).
    • (2015) Cancer Growth and Metastasis , vol.8 , pp. 35-42
    • Kumari, S.1    Malla, R.2
  • 58
    • 0028208353 scopus 로고
    • Serum interleukin 6 and C-reactive protein levels correlate with resistance to IL-2 therapy and poor survival in melanoma patients
    • Tartour, E. et al. Serum interleukin 6 and C-reactive protein levels correlate with resistance to IL-2 therapy and poor survival in melanoma patients. British journal of cancer 69, 911-913 (1994).
    • (1994) British Journal of Cancer , vol.69 , pp. 911-913
    • Tartour, E.1
  • 59
    • 33846948942 scopus 로고    scopus 로고
    • Loss of oncostatin M receptor beta in metastatic melanoma cells
    • Lacreusette, A. et al. Loss of oncostatin M receptor beta in metastatic melanoma cells. Oncogene 26, 881-892 (2007).
    • (2007) Oncogene , vol.26 , pp. 881-892
    • Lacreusette, A.1
  • 60
    • 84893862934 scopus 로고    scopus 로고
    • Oncostatin M receptor is a novel therapeutic target in cervical squamous cell carcinoma
    • Caffarel, M. M. & Coleman, N. Oncostatin M receptor is a novel therapeutic target in cervical squamous cell carcinoma. The Journal of pathology 232, 386-390 (2014).
    • (2014) The Journal of Pathology , vol.232 , pp. 386-390
    • Caffarel, M.M.1    Coleman, N.2
  • 61
    • 67650500874 scopus 로고    scopus 로고
    • Platelet-derived growth factor-receptor alpha strongly inhibits melanoma growth in vitro and in vivo
    • Faraone, D. et al. Platelet-derived growth factor-receptor alpha strongly inhibits melanoma growth in vitro and in vivo. Neoplasia (New York, NY) 11, 732-742 (2009).
    • (2009) Neoplasia (New York, NY) , vol.11 , pp. 732-742
    • Faraone, D.1
  • 62
    • 23844488162 scopus 로고    scopus 로고
    • Regulation of cancer cell motility through actin reorganization
    • Yamazaki, D., Kurisu, S. & Takenawa, T. Regulation of cancer cell motility through actin reorganization. Cancer science 96, 379-386 (2005).
    • (2005) Cancer Science , vol.96 , pp. 379-386
    • Yamazaki, D.1    Kurisu, S.2    Takenawa, T.3
  • 63
    • 84885611918 scopus 로고    scopus 로고
    • RAC1: An emerging therapeutic option for targeting cancer angiogenesis and metastasis
    • Bid, H. K., Roberts, R. D., Manchanda, P. K. & Houghton, P. J. RAC1: An emerging therapeutic option for targeting cancer angiogenesis and metastasis. Molecular Cancer Therapeutics 12, 1925-1934 (2013).
    • (2013) Molecular Cancer Therapeutics , vol.12 , pp. 1925-1934
    • Bid, H.K.1    Roberts, R.D.2    Manchanda, P.K.3    Houghton, P.J.4
  • 64
    • 67449124367 scopus 로고    scopus 로고
    • Activation of Rap1 promotes prostate cancer metastasis
    • Bailey, C. L., Kelly, P. & Casey, P. J. Activation of Rap1 promotes prostate cancer metastasis. Cancer research 69, 4962-4968 (2009).
    • (2009) Cancer Research , vol.69 , pp. 4962-4968
    • Bailey, C.L.1    Kelly, P.2    Casey, P.J.3
  • 65
    • 84929591055 scopus 로고    scopus 로고
    • Hypoxia/reoxygenation-experienced cancer cell migration and metastasis are regulated by Rap1-and Rac1-GTPase activation via the expression of thymosin beta-4
    • Lee, J.-W., Ryu, Y.-K., Ji, Y.-H., Kang, J. H. & Moon, E.-Y. Hypoxia/reoxygenation-experienced cancer cell migration and metastasis are regulated by Rap1-and Rac1-GTPase activation via the expression of thymosin beta-4. Oncotarget 6, 9820-9833 (2015).
    • (2015) Oncotarget , vol.6 , pp. 9820-9833
    • Lee, J.-W.1    Ryu, Y.-K.2    Ji, Y.-H.3    Kang, J.H.4    Moon, E.-Y.5
  • 66
    • 84875740623 scopus 로고    scopus 로고
    • P63 is an alternative p53 repressor in melanoma that confers chemoresistance and a poor prognosis
    • Matin, R. N. et al. p63 is an alternative p53 repressor in melanoma that confers chemoresistance and a poor prognosis. The Journal of experimental medicine 210, 581-603 (2013).
    • (2013) The Journal of Experimental Medicine , vol.210 , pp. 581-603
    • Matin, R.N.1
  • 67
    • 84905085953 scopus 로고    scopus 로고
    • TP63 and TP73 in cancer, an unresolved "family" puzzle of complexity, redundancy and hierarchy
    • Costanzo, A. et al. TP63 and TP73 in cancer, an unresolved "family" puzzle of complexity, redundancy and hierarchy. FEBS letters 588, 2590-2599 (2014).
    • (2014) FEBS Letters , vol.588 , pp. 2590-2599
    • Costanzo, A.1
  • 68
    • 85017538728 scopus 로고    scopus 로고
    • Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
    • Brammeld, J. S. et al. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations. Genome Research (2017).
    • (2017) Genome Research
    • Brammeld, J.S.1
  • 70
    • 0036206069 scopus 로고    scopus 로고
    • Guidelines for human gene nomenclature
    • Wain, H. M. et al. Guidelines for human gene nomenclature. Genomics 79, 464-470 (2002).
    • (2002) Genomics , vol.79 , pp. 464-470
    • Wain, H.M.1
  • 71
    • 84946040120 scopus 로고    scopus 로고
    • COSMIC: Exploring the world's knowledge of somatic mutations in human cancer
    • Forbes, S. A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Research 43, D805-11 (2015).
    • (2015) Nucleic Acids Research , vol.43 , pp. D805-D811
    • Forbes, S.A.1
  • 73
    • 84883467378 scopus 로고    scopus 로고
    • OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes
    • Tamborero, D., Gonzalez-Perez, A. & Lopez-Bigas, N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics 29, 2238-2244 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2238-2244
    • Tamborero, D.1    Gonzalez-Perez, A.2    Lopez-Bigas, N.3


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