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Volumn , Issue , 2015, Pages 84-95

Identifying mutation specific cancer pathways using a structurally resolved protein interaction network

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DISEASES;

EID: 84962882861     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper
Times cited : (8)

References (55)
  • 1
    • 84875490185 scopus 로고    scopus 로고
    • Cancer genome landscapes
    • Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558, doi:10.1126/science.1235122 (2013).
    • (2013) Science , vol.339 , pp. 1546-1558
    • Vogelstein, B.1
  • 2
    • 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, doi:10.1016/j.cell.2013.03.002 (2013).
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 4
    • 80052493684 scopus 로고    scopus 로고
    • A network-based approach to prioritize results from genome-wide association studies
    • Akula, N. et al. A network-based approach to prioritize results from genome-wide association studies. PloS one 6, e24220, doi:10.1371/journal.pone.0024220 (2011).
    • (2011) PloS One , vol.6 , pp. e24220
    • Akula, N.1
  • 6
    • 77949446630 scopus 로고    scopus 로고
    • Automated network analysis identifies core pathways in glioblastoma
    • Cerami, E., Demir, E., Schultz, N., Taylor, B. S.&Sander, C. Automated network analysis identifies core pathways in glioblastoma. PloS one 5, e8918, doi:10.1371/journal.pone.0008918 (2010).
    • (2010) PloS One , vol.5 , pp. e8918
    • Cerami, E.1    Demir, E.2    Schultz, N.3    Taylor, B.S.4    Sander, C.5
  • 7
    • 84887084951 scopus 로고    scopus 로고
    • Network-based stratification of tumor mutations
    • Hofree, M., Shen, J. P., Carter, H., Gross, A.&Ideker, T. Network-based stratification of tumor mutations. Nature methods 10, 1108-1115, doi:10.1038/nmeth.2651 (2013).
    • (2013) Nature Methods , vol.10 , pp. 1108-1115
    • Hofree, M.1    Shen, J.P.2    Carter, H.3    Gross, A.4    Ideker, T.5
  • 8
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • Mosca, R., Ceol, A.&Aloy, P. Interactome3D: adding structural details to protein networks. Nature methods 10, 47-53, doi:10.1038/nmeth.2289 (2013).
    • (2013) Nature Methods , vol.10 , pp. 47-53
    • Mosca, R.1    Ceol, A.2    Aloy, P.3
  • 9
    • 84863010950 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of protein networks provides insight into human genetic disease
    • Wang, X. et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature biotechnology 30, 159-164, doi:10.1038/nbt.2106 (2012).
    • (2012) Nature Biotechnology , vol.30 , pp. 159-164
    • Wang, X.1
  • 10
    • 84857790275 scopus 로고    scopus 로고
    • Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs
    • David, A., Razali, R., Wass, M. N.&Sternberg, M. J. Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Human mutation 33, 359-363, doi:10.1002/humu.21656 (2012).
    • (2012) Human Mutation , vol.33 , pp. 359-363
    • David, A.1    Razali, R.2    Wass, M.N.3    Sternberg, M.J.4
  • 11
    • 84894309512 scopus 로고    scopus 로고
    • Integrating structure to proteinprotein interaction networks that drive metastasis to brain and lung in breast cancer
    • Engin, H. B., Guney, E., Keskin, O., Oliva, B.&Gursoy, A. Integrating structure to proteinprotein interaction networks that drive metastasis to brain and lung in breast cancer. PloS one 8, e81035, doi:10.1371/journal.pone.0081035 (2013).
    • (2013) PloS One , vol.8 , pp. e81035
    • Engin, H.B.1    Guney, E.2    Keskin, O.3    Oliva, B.4    Gursoy, A.5
  • 12
    • 84907569494 scopus 로고    scopus 로고
    • The structural network of Interleukin-10 and its implications in inflammation and cancer
    • Acuner-Ozbabacan , S. E. et al. The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics 15, S2 (2014).
    • (2014) BMC Genomics , vol.15 , pp. S2
    • Acuner-Ozbabacan, S.E.1
  • 13
    • 84895765208 scopus 로고    scopus 로고
    • The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer
    • Acuner Ozbabacan, S. E., Gursoy, A., Nussinov, R.&Keskin, O. The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. PLoS computational biology 10, e1003470, doi:10.1371/journal.pcbi.1003470 (2014).
    • (2014) PLoS Computational Biology , vol.10 , pp. e1003470
    • Acuner Ozbabacan, S.E.1    Gursoy, A.2    Nussinov, R.3    Keskin, O.4
  • 14
    • 72849142731 scopus 로고    scopus 로고
    • Edgetic perturbation models of human inherited disorders
    • Zhong, Q. et al. Edgetic perturbation models of human inherited disorders. Molecular systems biology 5, 321, doi:10.1038/msb.2009.80 (2009).
    • (2009) Molecular Systems Biology , vol.5 , pp. 321
    • Zhong, Q.1
  • 15
    • 45949108954 scopus 로고    scopus 로고
    • Protein interactions in human genetic diseases
    • Schuster-Bockler, B.&Bateman, A. Protein interactions in human genetic diseases. Genome biology 9, R9, doi:10.1186/gb-2008-9-1-r9 (2008).
    • (2008) Genome Biology , vol.9 , pp. R9
    • Schuster-Bockler, B.1    Bateman, A.2
  • 16
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
    • Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic acids research 41, D808-815, doi:10.1093/nar/gks1094 (2013).
    • (2013) Nucleic Acids Research , vol.41 , pp. D808-D815
    • Franceschini, A.1
  • 17
    • 84864376672 scopus 로고    scopus 로고
    • HINT: High-quality protein interactomes and their applications in understanding human disease
    • Das, J.&Yu, H. HINT: High-quality protein interactomes and their applications in understanding human disease. BMC systems biology 6, 92, doi:10.1186/1752-0509-6-92 (2012).
    • (2012) BMC Systems Biology , vol.6 , pp. 92
    • Das, J.1    Yu, H.2
  • 18
    • 0017751668 scopus 로고
    • The protein data bank. A computer-based archival file for macromolecular structures
    • Bernstein, F. C. et al. The Protein Data Bank. A computer-based archival file for macromolecular structures. European journal of biochemistry / FEBS 80, 319-324 (1977).
    • (1977) European Journal of Biochemistry / FEBS , vol.80 , pp. 319-324
    • Bernstein, F.C.1
  • 19
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE project
    • Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 1760-1774, doi:10.1101/gr.135350.111 (2012).
    • (2012) Genome Research , vol.22 , pp. 1760-1774
    • Harrow, J.1
  • 20
    • 0037250168 scopus 로고    scopus 로고
    • The UCSC genome browser database
    • Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic acids research 31, 51-54 (2003).
    • (2003) Nucleic Acids Research , vol.31 , pp. 51-54
    • Karolchik, D.1
  • 21
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389-3402 (1997).
    • (1997) Nucleic Acids Research , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 22
    • 28444469788 scopus 로고    scopus 로고
    • Mapping PDB chains to UniProtKB entries
    • Martin, A. C. Mapping PDB chains to UniProtKB entries. Bioinformatics 21, 4297-4301, doi:10.1093/bioinformatics/bti694 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 4297-4301
    • Martin, A.C.1
  • 23
    • 77954294794 scopus 로고    scopus 로고
    • HotPoint: Hot spot prediction server for protein interfaces
    • Tuncbag, N., Keskin, O.&Gursoy, A. HotPoint: hot spot prediction server for protein interfaces. Nucleic acids research 38, W402-406, doi:10.1093/nar/gkq323 (2010).
    • (2010) Nucleic Acids Research , vol.38 , pp. W402-W406
    • Tuncbag, N.1    Keskin, O.2    Gursoy, A.3
  • 24
    • 80051576392 scopus 로고    scopus 로고
    • KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features
    • Zhu, X.&Mitchell, J. C. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins 79, 2671-2683, doi:10.1002/prot.23094 (2011).
    • (2011) Proteins , vol.79 , pp. 2671-2683
    • Zhu, X.1    Mitchell, J.C.2
  • 26
    • 76749134818 scopus 로고    scopus 로고
    • Associating genes and protein complexes with disease via network propagation
    • Vanunu, O., Magger, O., Ruppin, E., Shlomi, T.&Sharan, R. Associating genes and protein complexes with disease via network propagation. PLoS computational biology 6, e1000641, doi:10.1371/journal.pcbi.1000641 (2010).
    • (2010) PLoS Computational Biology , vol.6 , pp. e1000641
    • Vanunu, O.1    Magger, O.2    Ruppin, E.3    Shlomi, T.4    Sharan, R.5
  • 27
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome biology 5, R80, doi:10.1186/gb-2004-5-10-r80 (2004).
    • (2004) Genome Biology , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 29
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang da, W., Sherman, B. T.&Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 37, 1-13, doi:10.1093/nar/gkn923 (2009).
    • (2009) Nucleic Acids Research , vol.37 , pp. 1-13
    • Da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 30
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The gene ontology consortium
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29, doi:10.1038/75556 (2000).
    • (2000) Nature Genetics , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 31
    • 79960052850 scopus 로고    scopus 로고
    • Ras in cancer and developmental diseases
    • Fernandez-Medarde, A.&Santos, E. Ras in cancer and developmental diseases. Genes&cancer 2, 344-358, doi:10.1177/1947601911411084 (2011).
    • (2011) Genes&cancer , vol.2 , pp. 344-358
    • Fernandez-Medarde, A.1    Santos, E.2
  • 32
    • 20044363093 scopus 로고    scopus 로고
    • Replacement of K-ras with H-ras supports normal embryonic development despite inducing cardiovascular pathology in adult mice
    • Potenza, N. et al. Replacement of K-Ras with H-Ras supports normal embryonic development despite inducing cardiovascular pathology in adult mice. EMBO reports 6, 432-437, doi:10.1038/sj.embor.7400397 (2005).
    • (2005) EMBO Reports , vol.6 , pp. 432-437
    • Potenza, N.1
  • 33
    • 77955277111 scopus 로고    scopus 로고
    • Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: A retrospective consortium analysis
    • De Roock, W. et al. Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. The lancet oncology 11, 753-762, doi:10.1016/S1470-2045(10)70130-3 (2010).
    • (2010) The Lancet Oncology , vol.11 , pp. 753-762
    • De Roock, W.1
  • 34
    • 0035475987 scopus 로고    scopus 로고
    • The role of the coagulation system in tumour angiogenesis
    • Nash, G. F., Walsh, D. C.&Kakkar, A. K. The role of the coagulation system in tumour angiogenesis. The lancet oncology 2, 608-613 (2001).
    • (2001) The Lancet Oncology , vol.2 , pp. 608-613
    • Nash, G.F.1    Walsh, D.C.2    Kakkar, A.K.3
  • 35
    • 77949697909 scopus 로고    scopus 로고
    • Inhibition of vasculogenesis, but not angiogenesis, prevents the recurrence of glioblastoma after irradiation in mice
    • Kioi, M. et al. Inhibition of vasculogenesis, but not angiogenesis, prevents the recurrence of glioblastoma after irradiation in mice. The Journal of clinical investigation 120, 694-705, doi:10.1172/JCI40283 (2010).
    • (2010) The Journal of Clinical Investigation , vol.120 , pp. 694-705
    • Kioi, M.1
  • 36
    • 0032512655 scopus 로고    scopus 로고
    • Chemokine receptors in human endothelial cells. Functional expression of CXCR4 and its transcriptional regulation by inflammatory cytokines
    • Gupta, S. K., Lysko, P. G., Pillarisetti, K., Ohlstein, E.&Stadel, J. M. Chemokine receptors in human endothelial cells. Functional expression of CXCR4 and its transcriptional regulation by inflammatory cytokines. The Journal of biological chemistry 273, 4282-4287 (1998).
    • (1998) The Journal of Biological Chemistry , vol.273 , pp. 4282-4287
    • Gupta, S.K.1    Lysko, P.G.2    Pillarisetti, K.3    Ohlstein, E.4    Stadel, J.M.5
  • 37
    • 0034076189 scopus 로고    scopus 로고
    • Mechanisms of angiogenesis and arteriogenesis
    • Carmeliet, P. Mechanisms of angiogenesis and arteriogenesis. Nature medicine 6, 389-395, doi:10.1038/74651 (2000).
    • (2000) Nature Medicine , vol.6 , pp. 389-395
    • Carmeliet, P.1
  • 38
    • 70849134402 scopus 로고    scopus 로고
    • ELR+ CXC chemokines and oncogenic Rasmediated tumorigenesis
    • O'Hayer, K. M., Brady, D. C.&Counter, C. M. ELR+ CXC chemokines and oncogenic Rasmediated tumorigenesis. Carcinogenesis 30, 1841-1847, doi:10.1093/carcin/bgp198 (2009).
    • (2009) Carcinogenesis , vol.30 , pp. 1841-1847
    • O'Hayer, K.M.1    Brady, D.C.2    Counter, C.M.3
  • 39
    • 0033614962 scopus 로고    scopus 로고
    • Essential role for oncogenic Ras in tumour maintenance
    • Chin, L. et al. Essential role for oncogenic Ras in tumour maintenance. Nature 400, 468-472, doi:10.1038/22788 (1999).
    • (1999) Nature , vol.400 , pp. 468-472
    • Chin, L.1
  • 42
    • 79251647799 scopus 로고    scopus 로고
    • Interferon-gamma links ultraviolet radiation to melanomagenesis in mice
    • Zaidi, M. R. et al. Interferon-gamma links ultraviolet radiation to melanomagenesis in mice. Nature 469, 548-553, doi:10.1038/nature09666 (2011).
    • (2011) Nature , vol.469 , pp. 548-553
    • Zaidi, M.R.1
  • 43
    • 84895871023 scopus 로고    scopus 로고
    • Ultraviolet-radiation-induced inflammation promotes angiotropism and metastasis in melanoma
    • Bald, T. et al. Ultraviolet-radiation-induced inflammation promotes angiotropism and metastasis in melanoma. Nature 507, 109-113, doi:10.1038/nature13111 (2014).
    • (2014) Nature , vol.507 , pp. 109-113
    • Bald, T.1
  • 44
    • 34250831624 scopus 로고    scopus 로고
    • Loss of xeroderma pigmentosum C (Xpc) enhances melanoma photocarcinogenesis in Ink4a-arf-deficient mice
    • Yang, G., Curley, D., Bosenberg, M. W.&Tsao, H. Loss of xeroderma pigmentosum C (Xpc) enhances melanoma photocarcinogenesis in Ink4a-Arf-deficient mice. Cancer research 67, 5649-5657, doi:10.1158/0008-5472.CAN-06-3806 (2007).
    • (2007) Cancer Research , vol.67 , pp. 5649-5657
    • Yang, G.1    Curley, D.2    Bosenberg, M.W.3    Tsao, H.4
  • 45
    • 0026730948 scopus 로고
    • Mapping of UV photoproducts within ras proto-oncogenes in UV-irradiated cells: Correlation with mutations in human skin cancer
    • Tormanen, V. T.&Pfeifer, G. P. Mapping of UV photoproducts within ras proto-oncogenes in UV-irradiated cells: correlation with mutations in human skin cancer. Oncogene 7, 1729-1736 (1992).
    • (1992) Oncogene , vol.7 , pp. 1729-1736
    • Tormanen, V.T.1    Pfeifer, G.P.2
  • 46
    • 56049114699 scopus 로고    scopus 로고
    • Many faces of ras activation
    • Buday, L.&Downward, J. Many faces of Ras activation. Biochimica et biophysica acta 1786, 178-187, doi:10.1016/j.bbcan.2008.05.001 (2008).
    • (2008) Biochimica et Biophysica Acta , vol.1786 , pp. 178-187
    • Buday, L.1    Downward, J.2
  • 47
    • 60749118005 scopus 로고    scopus 로고
    • A missense mutation in the APC tumor suppressor gene disrupts an ASF/SF2 splicing enhancer motif and causes pathogenic skipping of exon 14
    • Goncalves, V. et al. A missense mutation in the APC tumor suppressor gene disrupts an ASF/SF2 splicing enhancer motif and causes pathogenic skipping of exon 14. Mutation research 662, 33-36, doi:10.1016/j.mrfmmm.2008.12.001 (2009).
    • (2009) Mutation Research , vol.662 , pp. 33-36
    • Goncalves, V.1
  • 48
    • 0033883092 scopus 로고    scopus 로고
    • APC mutations in sporadic medulloblastomas
    • Huang, H. et al. APC mutations in sporadic medulloblastomas. The American journal of pathology 156, 433-437, doi:10.1016/S0002-9440(10)64747-5 (2000).
    • (2000) The American Journal of Pathology , vol.156 , pp. 433-437
    • Huang, H.1
  • 49
    • 79960063257 scopus 로고    scopus 로고
    • Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin
    • Eustermann, S. et al. Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nature structural&molecular biology 18, 777-782, doi:10.1038/nsmb.2070 (2011).
    • (2011) Nature Structural&molecular Biology , vol.18 , pp. 777-782
    • Eustermann, S.1
  • 51
    • 25144497571 scopus 로고    scopus 로고
    • The BRCA1-interacting helicase BRIP1 is deficient in fanconi anemia
    • Levran, O. et al. The BRCA1-interacting helicase BRIP1 is deficient in Fanconi anemia. Nature genetics 37, 931-933, doi:10.1038/ng1624 (2005).
    • (2005) Nature Genetics , vol.37 , pp. 931-933
    • Levran, O.1
  • 52
    • 84555196106 scopus 로고    scopus 로고
    • BRCA1 and BRCA2: Different roles in a common pathway of genome protection
    • Roy, R., Chun, J.&Powell, S. N. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nature reviews. Cancer 12, 68-78, doi:10.1038/nrc3181 (2012).
    • (2012) Nature Reviews. Cancer , vol.12 , pp. 68-78
    • Roy, R.1    Chun, J.2    Powell, S.N.3
  • 53
    • 33847314487 scopus 로고    scopus 로고
    • Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis
    • Carvalho, M. A. et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer research 67, 1494-1501, doi:10.1158/0008-5472.CAN-06-3297 (2007).
    • (2007) Cancer Research , vol.67 , pp. 1494-1501
    • Carvalho, M.A.1
  • 54
    • 84863786019 scopus 로고    scopus 로고
    • CBL mutation-related patterns of phosphorylation and sensitivity to tyrosine kinase inhibitors
    • Makishima, H. et al. CBL mutation-related patterns of phosphorylation and sensitivity to tyrosine kinase inhibitors. Leukemia 26, 1547-1554, doi:10.1038/leu.2012.7 (2012).
    • (2012) Leukemia , vol.26 , pp. 1547-1554
    • Makishima, H.1
  • 55
    • 0033602144 scopus 로고    scopus 로고
    • A direct interaction between the adaptor protein Cbl-b and the kinase zap-70 induces a positive signal in T cells
    • Zhang, Z., Elly, C., Qiu, L., Altman, A.&Liu, Y. C. A direct interaction between the adaptor protein Cbl-b and the kinase zap-70 induces a positive signal in T cells. Current biology : CB 9, 203-206 (1999).
    • (1999) Current Biology : CB , vol.9 , pp. 203-206
    • Zhang, Z.1    Elly, C.2    Qiu, L.3    Altman, A.4    Liu, Y.C.5


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