메뉴 건너뛰기




Volumn 14, Issue 9, 2015, Pages 3555-3567

Advanced proteogenomic analysis reveals multiple peptide mutations and complex immunoglobulin peptides in colon cancer

Author keywords

cancer; cancer proteogenomics; CPTAC; Proteogenomics; RNA seq; TCGA

Indexed keywords

IMMUNOGLOBULIN; PEPTIDE;

EID: 84941099453     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00264     Document Type: Article
Times cited : (29)

References (55)
  • 1
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Koboldt, D. C.; Fulton, R. S.; McLellan, M. D.; Schmidt, H. et al. Comprehensive molecular portraits of human breast tumours Nature 2012, 490, 61-70 10.1038/nature11412
    • (2012) Nature , vol.490 , pp. 61-70
    • Koboldt, D.C.1    Fulton, R.S.2    McLellan, M.D.3    Schmidt, H.4
  • 2
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • Bell, D.; Berchuck, A.; Birrer, M.; Chien, J. et al. Integrated genomic analyses of ovarian carcinoma Nature 2011, 474, 609-615 10.1038/nature10166
    • (2011) Nature , vol.474 , pp. 609-615
    • Bell, D.1    Berchuck, A.2    Birrer, M.3    Chien, J.4
  • 3
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • Muzny, D. M. et al. Comprehensive molecular characterization of human colon and rectal cancer Nature 2012, 487, 330-337 10.1038/nature11252
    • (2012) Nature , vol.487 , pp. 330-337
    • Muzny, D.M.1
  • 5
    • 84907269780 scopus 로고    scopus 로고
    • Proteogenomic characterization of human colon and rectal cancer
    • Zhang, B. et al. Proteogenomic characterization of human colon and rectal cancer Nature 2014, 513, 382-387 10.1038/nature13438
    • (2014) Nature , vol.513 , pp. 382-387
    • Zhang, B.1
  • 6
    • 84891801883 scopus 로고    scopus 로고
    • Proteogenomic database construction driven from large scale RNA-seq data
    • Woo, S.; Cha, S. W.; Merrihew, G.; He, Y. et al. Proteogenomic database construction driven from large scale RNA-seq data J. Proteome Res. 2014, 13, 21-28 10.1021/pr400294c
    • (2014) J. Proteome Res. , vol.13 , pp. 21-28
    • Woo, S.1    Cha, S.W.2    Merrihew, G.3    He, Y.4
  • 7
    • 84914159272 scopus 로고    scopus 로고
    • Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data
    • Woo, S.; Cha, S. W. et al. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data Proteomics 2014, 14, 2719-2730 10.1002/pmic.201400206
    • (2014) Proteomics , vol.14 , pp. 2719-2730
    • Woo, S.1    Cha, S.W.2
  • 8
    • 84891760451 scopus 로고    scopus 로고
    • An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays
    • Castellana, N. E.; Shen, Z.; He, Y.; Walley, J. W. et al. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays Mol. Cell. Proteomics 2014, 13, 157-167 10.1074/mcp.M113.031260
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 157-167
    • Castellana, N.E.1    Shen, Z.2    He, Y.3    Walley, J.W.4
  • 9
    • 77957237701 scopus 로고    scopus 로고
    • Proteogenomics to discover the full coding content of genomes: A computational perspective
    • Castellana, N.; Bafna, V. Proteogenomics to discover the full coding content of genomes: a computational perspective J. Proteomics 2010, 73, 2124-2135 10.1016/j.jprot.2010.06.007
    • (2010) J. Proteomics , vol.73 , pp. 2124-2135
    • Castellana, N.1    Bafna, V.2
  • 10
    • 84908540871 scopus 로고    scopus 로고
    • Proteogenomics: Concepts, applications and computational strategies
    • Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11, 1114-1125 10.1038/nmeth.3144
    • (2014) Nat. Methods , vol.11 , pp. 1114-1125
    • Nesvizhskii, A.I.1
  • 13
    • 77149126695 scopus 로고    scopus 로고
    • CanProVar: A human cancer proteome variation database
    • Li, J.; Duncan, D. T.; Zhang, B. CanProVar: a human cancer proteome variation database Hum. Mutat. 2010, 31, 219-228 10.1002/humu.21176
    • (2010) Hum. Mutat. , vol.31 , pp. 219-228
    • Li, J.1    Duncan, D.T.2    Zhang, B.3
  • 14
    • 79955765660 scopus 로고    scopus 로고
    • A bioinformatics workflow for variant peptide detection in shotgun proteomics
    • Li, J.; Su, Z.; Ma, Z. Q.; Slebos, R. J. et al. A bioinformatics workflow for variant peptide detection in shotgun proteomics Mol. Cell. Proteomics 2011, 10, M110.006536 10.1074/mcp.M110.006536
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. 110006536
    • Li, J.1    Su, Z.2    Ma, Z.Q.3    Slebos, R.J.4
  • 15
    • 84863011504 scopus 로고    scopus 로고
    • Protein identification using customized protein sequence databases derived from RNA-Seq data
    • Wang, X.; Slebos, R. J.; Wang, D.; Halvey, P. J. et al. Protein identification using customized protein sequence databases derived from RNA-Seq data J. Proteome Res. 2012, 11, 1009-1017 10.1021/pr200766z
    • (2012) J. Proteome Res. , vol.11 , pp. 1009-1017
    • Wang, X.1    Slebos, R.J.2    Wang, D.3    Halvey, P.J.4
  • 16
    • 84894110748 scopus 로고    scopus 로고
    • CustomProDB: An R package to generate customized protein databases from RNA-Seq data for proteomics search
    • Wang, X.; Zhang, B. customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search Bioinformatics 2013, 29, 3235-3237 10.1093/bioinformatics/btt543
    • (2013) Bioinformatics , vol.29 , pp. 3235-3237
    • Wang, X.1    Zhang, B.2
  • 17
    • 79751489596 scopus 로고    scopus 로고
    • Molecular genetics of colorectal cancer
    • Fearon, E. R. Molecular genetics of colorectal cancer Annu. Rev. Pathol.: Mech. Dis. 2011, 6, 479-507 10.1146/annurev-pathol-011110-130235
    • (2011) Annu. Rev. Pathol.: Mech. Dis. , vol.6 , pp. 479-507
    • Fearon, E.R.1
  • 18
    • 58549101102 scopus 로고    scopus 로고
    • Discovery and revision of Arabidopsis genes by proteogenomics
    • Castellana, N. E.; Payne, S. H.; Shen, Z.; Stanke, M. et al. Discovery and revision of Arabidopsis genes by proteogenomics Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 21034-21038 10.1073/pnas.0811066106
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 21034-21038
    • Castellana, N.E.1    Payne, S.H.2    Shen, Z.3    Stanke, M.4
  • 19
    • 0038407404 scopus 로고    scopus 로고
    • Antigen-driven clonal proliferation, somatic hypermutation, and selection of B lymphocytes infiltrating human ductal breast carcinomas
    • Nzula, S.; Going, J. J.; Stott, D. I. Antigen-driven clonal proliferation, somatic hypermutation, and selection of B lymphocytes infiltrating human ductal breast carcinomas Cancer Res. 2003, 63, 3275-3280
    • (2003) Cancer Res. , vol.63 , pp. 3275-3280
    • Nzula, S.1    Going, J.J.2    Stott, D.I.3
  • 20
    • 78149488860 scopus 로고    scopus 로고
    • CD20+ B cells: The other tumor-infiltrating lymphocytes
    • Nelson, B. H. CD20+ B cells: the other tumor-infiltrating lymphocytes J. Immunol. 2010, 185, 4977-4982 10.4049/jimmunol.1001323
    • (2010) J. Immunol. , vol.185 , pp. 4977-4982
    • Nelson, B.H.1
  • 22
  • 23
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R.; Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res. 2008, 18, 821-829 10.1101/gr.074492.107
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 24
    • 80755159050 scopus 로고    scopus 로고
    • How to apply de Bruijn graphs to genome assembly
    • Compeau, P. E.; Pevzner, P. A.; Tesler, G. How to apply de Bruijn graphs to genome assembly Nat. Biotechnol. 2011, 29, 987-991 10.1038/nbt.2023
    • (2011) Nat. Biotechnol. , vol.29 , pp. 987-991
    • Compeau, P.E.1    Pevzner, P.A.2    Tesler, G.3
  • 25
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M. S. et al. A draft map of the human proteome Nature 2014, 509, 575-581 10.1038/nature13302
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1
  • 26
    • 84875931748 scopus 로고    scopus 로고
    • Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405
    • Fanayan, S.; Smith, J. T.; Lee, L. Y.; Yan, F.; Snyder, M.; Hancock, W. S.; Nice, E. Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405 J. Proteome Res. 2013, 12, 1732-1742 10.1021/pr3010869
    • (2013) J. Proteome Res. , vol.12 , pp. 1732-1742
    • Fanayan, S.1    Smith, J.T.2    Lee, L.Y.3    Yan, F.4    Snyder, M.5    Hancock, W.S.6    Nice, E.7
  • 28
    • 84879912851 scopus 로고    scopus 로고
    • IDBA-tran: A more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
    • Peng, Y.; Leung, H. C.; Yiu, S.-M.; Lv, M.-J.; Zhu, X.-G.; Chin, F. Y. IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels Bioinformatics 2013, 29, i326-i334 10.1093/bioinformatics/btt219
    • (2013) Bioinformatics , vol.29 , pp. 326-i334
    • Peng, Y.1    Leung, H.C.2    Yiu, S.-M.3    Lv, M.-J.4    Zhu, X.-G.5    Chin, F.Y.6
  • 29
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A.; Hanna, M.; Banks, E.; Sivachenko, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 2010, 20, 1297-1303 10.1101/gr.107524.110
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4
  • 30
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A.; Banks, E.; Poplin, R.; Garimella, K. V. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat. Genet. 2011, 43, 491-498 10.1038/ng.806
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4
  • 31
    • 78650147228 scopus 로고    scopus 로고
    • The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: Applications to database search
    • Kim, S.; Mischerikow, N.; Bandeira, N.; Navarro, J. D. et al. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search Mol. Cell. Proteomics 2010, 9, 2840-2852 10.1074/mcp.M110.003731
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 2840-2852
    • Kim, S.1    Mischerikow, N.2    Bandeira, N.3    Navarro, J.D.4
  • 32
    • 84923247212 scopus 로고    scopus 로고
    • MS-GF+ makes progress towards a universal database search tool for proteomics
    • Kim, S.; Pevzner, P. A. MS-GF+ makes progress towards a universal database search tool for proteomics Nat. Commun. 2014, 5, 5277 10.1038/ncomms6277
    • (2014) Nat. Commun. , vol.5 , pp. 5277
    • Kim, S.1    Pevzner, P.A.2
  • 33
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4, 207-214 10.1038/nmeth1019
    • (2007) Nat. Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 34
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: Current status, policy and new initiatives
    • Pruitt, K. D.; Tatusova, T.; Klimke, W.; Maglott, D. R. NCBI Reference Sequences: current status, policy and new initiatives Nucleic Acids Res. 2009, 37, D32-36 10.1093/nar/gkn721
    • (2009) Nucleic Acids Res. , vol.37 , pp. 32-36
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 35
    • 0035173378 scopus 로고    scopus 로고
    • DbSNP: The NCBI database of genetic variation
    • Sherry, S. T.; Ward, M. H.; Kholodov, M.; Baker, J. et al. dbSNP: the NCBI database of genetic variation Nucleic Acids Res. 2001, 29, 308-311 10.1093/nar/29.1.308
    • (2001) Nucleic Acids Res. , vol.29 , pp. 308-311
    • Sherry, S.T.1    Ward, M.H.2    Kholodov, M.3    Baker, J.4
  • 36
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes, S. A.; Bindal, N.; Bamford, S.; Cole, C. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer Nucleic Acids Res. 2011, 39, D945-950 10.1093/nar/gkq929
    • (2011) Nucleic Acids Res. , vol.39 , pp. 945-950
    • Forbes, S.A.1    Bindal, N.2    Bamford, S.3    Cole, C.4
  • 38
    • 84872371907 scopus 로고    scopus 로고
    • Comet: An open-source MS/MS sequence database search tool
    • Eng, J. K.; Jahan, T. A.; Hoopmann, M. R. Comet: an open-source MS/MS sequence database search tool Proteomics 2013, 13, 22-24 10.1002/pmic.201200439
    • (2013) Proteomics , vol.13 , pp. 22-24
    • Eng, J.K.1    Jahan, T.A.2    Hoopmann, M.R.3
  • 39
    • 84878177246 scopus 로고    scopus 로고
    • Tumor-derived tenascin-C promotes the epithelial-mesenchymal transition in colorectal cancer cells
    • Takahashi, Y. et al. Tumor-derived tenascin-C promotes the epithelial-mesenchymal transition in colorectal cancer cells Anticancer Res. 2013, 33, 1927-1934
    • (2013) Anticancer Res. , vol.33 , pp. 1927-1934
    • Takahashi, Y.1
  • 40
    • 0344393418 scopus 로고    scopus 로고
    • Perlecan and tumor angiogenesis
    • Jiang, X.; Couchman, J. R. Perlecan and tumor angiogenesis J. Histochem. Cytochem. 2003, 51, 1393-1410 10.1177/002215540305101101
    • (2003) J. Histochem. Cytochem. , vol.51 , pp. 1393-1410
    • Jiang, X.1    Couchman, J.R.2
  • 41
    • 84155184254 scopus 로고    scopus 로고
    • PML as a potential predictive factor of oxaliplatin/fluoropyrimidine-based first line chemotherapy efficacy in colorectal cancer patients
    • Vincenzi, B. et al. PML as a potential predictive factor of oxaliplatin/fluoropyrimidine-based first line chemotherapy efficacy in colorectal cancer patients J. Cell. Physiol. 2012, 227, 927-933 10.1002/jcp.22801
    • (2012) J. Cell. Physiol. , vol.227 , pp. 927-933
    • Vincenzi, B.1
  • 43
    • 68949128854 scopus 로고    scopus 로고
    • Transferrin dipstick as a potential novel test for colon cancer screening: A comparative study with immuno fecal occult blood test
    • Sheng, J. Q.; Li, S. R.; Wu, Z. T.; Xia, C. H.; Wu, X.; Chen, J.; Rao, J. Transferrin dipstick as a potential novel test for colon cancer screening: a comparative study with immuno fecal occult blood test Cancer Epidemiol., Biomarkers Prev. 2009, 18, 2182-2185 10.1158/1055-9965.EPI-09-0309
    • (2009) Cancer Epidemiol., Biomarkers Prev. , vol.18 , pp. 2182-2185
    • Sheng, J.Q.1    Li, S.R.2    Wu, Z.T.3    Xia, C.H.4    Wu, X.5    Chen, J.6    Rao, J.7
  • 46
    • 84862557227 scopus 로고    scopus 로고
    • CD20+ tumor-infiltrating lymphocytes have an atypical CD27- memory phenotype and together with CD8+ T cells promote favorable prognosis in ovarian cancer
    • Nielsen, J. S.; Sahota, R. A.; Milne, K.; Kost, S. E.; Nesslinger, N. J.; Watson, P. H.; Nelson, B. H. CD20+ tumor-infiltrating lymphocytes have an atypical CD27- memory phenotype and together with CD8+ T cells promote favorable prognosis in ovarian cancer Clin. Cancer Res. 2012, 18, 3281-3292 10.1158/1078-0432.CCR-12-0234
    • (2012) Clin. Cancer Res. , vol.18 , pp. 3281-3292
    • Nielsen, J.S.1    Sahota, R.A.2    Milne, K.3    Kost, S.E.4    Nesslinger, N.J.5    Watson, P.H.6    Nelson, B.H.7
  • 47
    • 84877619075 scopus 로고    scopus 로고
    • A colorectal cancer classification system that associates cellular phenotype and responses to therapy
    • Sadanandam, A. et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy Nat. Med. 2013, 19, 619-625 10.1038/nm.3175
    • (2013) Nat. Med. , vol.19 , pp. 619-625
    • Sadanandam, A.1
  • 48
    • 84877600884 scopus 로고    scopus 로고
    • Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions
    • de Sousa E Melo, F. et al. Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions Nat. Med. 2013, 19, 614-618 10.1038/nm.3174
    • (2013) Nat. Med. , vol.19 , pp. 614-618
    • De Sousa Melo E, F.1
  • 49
    • 0037757793 scopus 로고    scopus 로고
    • Role of Smad4 (DPC4) inactivation in human cancer
    • Miyaki, M.; Kuroki, T. Role of Smad4 (DPC4) inactivation in human cancer Biochem. Biophys. Res. Commun. 2003, 306, 799-804 10.1016/S0006-291X(03)01066-0
    • (2003) Biochem. Biophys. Res. Commun. , vol.306 , pp. 799-804
    • Miyaki, M.1    Kuroki, T.2
  • 50
    • 0035678764 scopus 로고    scopus 로고
    • SMAD4/DPC4 and pancreatic cancer survival. Commentary re: M. Tascilar et al., the SMAD4 protein and prognosis of pancreatic ductal adenocarcinoma. Clin. Cancer Res., 7:4115-4121, 2001
    • Liu, F. SMAD4/DPC4 and pancreatic cancer survival. Commentary re: M. Tascilar et al., The SMAD4 protein and prognosis of pancreatic ductal adenocarcinoma. Clin. Cancer Res., 7:4115-4121, 2001 Clin. Cancer Res. 2001, 7, 3853-3856
    • (2001) Clin. Cancer Res. , vol.7 , pp. 3853-3856
    • Liu, F.1
  • 52
    • 81855166106 scopus 로고    scopus 로고
    • The role of polymeric immunoglobulin receptor in inflammation-induced tumor metastasis of human hepatocellular carcinoma
    • Ai, J. et al. The role of polymeric immunoglobulin receptor in inflammation-induced tumor metastasis of human hepatocellular carcinoma J. Natl. Cancer Inst. 2011, 103, 1696-1712 10.1093/jnci/djr360
    • (2011) J. Natl. Cancer Inst. , vol.103 , pp. 1696-1712
    • Ai, J.1
  • 53
    • 84861057905 scopus 로고    scopus 로고
    • Identifying FGA peptides as nasopharyngeal carcinoma-associated biomarkers by magnetic beads
    • Tao, Y. L. et al. Identifying FGA peptides as nasopharyngeal carcinoma-associated biomarkers by magnetic beads J. Cell. Biochem. 2012, 113, 2268-2278 10.1002/jcb.24097
    • (2012) J. Cell. Biochem. , vol.113 , pp. 2268-2278
    • Tao, Y.L.1
  • 54
    • 84891767394 scopus 로고    scopus 로고
    • RefSeq: An update on mammalian reference sequences
    • Pruitt, K. D. et al. RefSeq: an update on mammalian reference sequences Nucleic Acids Res. 2014, 42, D756-763 10.1093/nar/gkt1114
    • (2014) Nucleic Acids Res. , vol.42 , pp. 756-763
    • Pruitt, K.D.1
  • 55
    • 84872593801 scopus 로고    scopus 로고
    • Characterization of adult α- And β-globin elevated by hydrogen peroxide in cervical cancer cells that play a cytoprotective role against oxidative insults
    • Li, X.; Wu, Z.; Wang, Y.; Mei, Q.; Fu, X.; Han, W. Characterization of adult α- and β-globin elevated by hydrogen peroxide in cervical cancer cells that play a cytoprotective role against oxidative insults PLoS One 2013, 8, e54342 10.1371/journal.pone.0054342
    • (2013) PLoS One , vol.8 , pp. 54342
    • Li, X.1    Wu, Z.2    Wang, Y.3    Mei, Q.4    Fu, X.5    Han, W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.