@article{RN6158,
   author = {Akbani, R. and Ng, P. K. and Werner, H. M. and Shahmoradgoli, M. and Zhang, F. and Ju, Z. and Liu, W. and Yang, J. Y. and Yoshihara, K. and Li, J. and Ling, S. and Seviour, E. G. and Ram, P. T. and Minna, J. D. and Diao, L. and Tong, P. and Heymach, J. V. and Hill, S. M. and Dondelinger, F. and Städler, N. and Byers, L. A. and Meric-Bernstam, F. and Weinstein, J. N. and Broom, B. M. and Verhaak, R. G. and Liang, H. and Mukherjee, S. and Lu, Y. and Mills, G. B.},
   title = {A pan-cancer proteomic perspective on The Cancer Genome Atlas},
   journal = {Nat Commun},
   volume = {5},
   pages = {3887},
   note = {2041-1723
Akbani, Rehan
Ng, Patrick Kwok Shing
Werner, Henrica M J
Shahmoradgoli, Maria
Zhang, Fan
Ju, Zhenlin
Liu, Wenbin
Yang, Ji-Yeon
Yoshihara, Kosuke
Li, Jun
Ling, Shiyun
Seviour, Elena G
Ram, Prahlad T
Minna, John D
Diao, Lixia
Tong, Pan
Heymach, John V
Hill, Steven M
Dondelinger, Frank
Städler, Nicolas
Byers, Lauren A
Meric-Bernstam, Funda
Weinstein, John N
Broom, Bradley M
Verhaak, Roeland G W
Liang, Han
Mukherjee, Sach
Lu, Yiling
Mills, Gordon B
P30 CA016672/CA/NCI NIH HHS/United States
P50 CA100632/CA/NCI NIH HHS/United States
U54 CA112970/CA/NCI NIH HHS/United States
TCGA CA143883/CA/NCI NIH HHS/United States
U24 CA143883/CA/NCI NIH HHS/United States
NCI P50CA70907/CA/NCI NIH HHS/United States
MC_UP_1302/1/MRC_/Medical Research Council/United Kingdom
P50 CA098258/CA/NCI NIH HHS/United States
U01 CA168394/CA/NCI NIH HHS/United States
P50 CA083639/CA/NCI NIH HHS/United States
NCI U54 CA112970/CA/NCI NIH HHS/United States
P50 CA070907/CA/NCI NIH HHS/United States
U01 CA176284/CA/NCI NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
England
2014/05/30
Nat Commun. 2014 May 29;5:3887. doi: 10.1038/ncomms4887.},
   abstract = {Protein levels and function are poorly predicted by genomic and transcriptomic analysis of patient tumours. Therefore, direct study of the functional proteome has the potential to provide a wealth of information that complements and extends genomic, epigenomic and transcriptomic analysis in The Cancer Genome Atlas (TCGA) projects. Here we use reverse-phase protein arrays to analyse 3,467 patient samples from 11 TCGA 'Pan-Cancer' diseases, using 181 high-quality antibodies that target 128 total proteins and 53 post-translationally modified proteins. The resultant proteomic data are integrated with genomic and transcriptomic analyses of the same samples to identify commonalities, differences, emergent pathways and network biology within and across tumour lineages. In addition, tissue-specific signals are reduced computationally to enhance biomarker and target discovery spanning multiple tumour lineages. This integrative analysis, with an emphasis on pathways and potentially actionable proteins, provides a framework for determining the prognostic, predictive and therapeutic relevance of the functional proteome.},
   keywords = {Cluster Analysis
Gene Dosage
*Genome, Human
Humans
Neoplasm Proteins/genetics/*metabolism
Neoplasms/*genetics
Organ Specificity
*Proteomics
RNA, Messenger/genetics/metabolism
Receptor, ErbB-2/genetics/metabolism
Signal Transduction/genetics
Statistics, Nonparametric},
   ISSN = {2041-1723},
   DOI = {10.1038/ncomms4887},
   year = {2014},
   type = {Journal Article}
}

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B."],"bibdata":{"bibtype":"article","type":"Journal Article","author":[{"propositions":[],"lastnames":["Akbani"],"firstnames":["R."],"suffixes":[]},{"propositions":[],"lastnames":["Ng"],"firstnames":["P.","K."],"suffixes":[]},{"propositions":[],"lastnames":["Werner"],"firstnames":["H.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Shahmoradgoli"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["F."],"suffixes":[]},{"propositions":[],"lastnames":["Ju"],"firstnames":["Z."],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["W."],"suffixes":[]},{"propositions":[],"lastnames":["Yang"],"firstnames":["J.","Y."],"suffixes":[]},{"propositions":[],"lastnames":["Yoshihara"],"firstnames":["K."],"suffixes":[]},{"propositions":[],"lastnames":["Li"],"firstnames":["J."],"suffixes":[]},{"propositions":[],"lastnames":["Ling"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Seviour"],"firstnames":["E.","G."],"suffixes":[]},{"propositions":[],"lastnames":["Ram"],"firstnames":["P.","T."],"suffixes":[]},{"propositions":[],"lastnames":["Minna"],"firstnames":["J.","D."],"suffixes":[]},{"propositions":[],"lastnames":["Diao"],"firstnames":["L."],"suffixes":[]},{"propositions":[],"lastnames":["Tong"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Heymach"],"firstnames":["J.","V."],"suffixes":[]},{"propositions":[],"lastnames":["Hill"],"firstnames":["S.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Dondelinger"],"firstnames":["F."],"suffixes":[]},{"propositions":[],"lastnames":["Städler"],"firstnames":["N."],"suffixes":[]},{"propositions":[],"lastnames":["Byers"],"firstnames":["L.","A."],"suffixes":[]},{"propositions":[],"lastnames":["Meric-Bernstam"],"firstnames":["F."],"suffixes":[]},{"propositions":[],"lastnames":["Weinstein"],"firstnames":["J.","N."],"suffixes":[]},{"propositions":[],"lastnames":["Broom"],"firstnames":["B.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Verhaak"],"firstnames":["R.","G."],"suffixes":[]},{"propositions":[],"lastnames":["Liang"],"firstnames":["H."],"suffixes":[]},{"propositions":[],"lastnames":["Mukherjee"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Lu"],"firstnames":["Y."],"suffixes":[]},{"propositions":[],"lastnames":["Mills"],"firstnames":["G.","B."],"suffixes":[]}],"title":"A pan-cancer proteomic perspective on The Cancer Genome Atlas","journal":"Nat Commun","volume":"5","pages":"3887","note":"2041-1723 Akbani, Rehan Ng, Patrick Kwok Shing Werner, Henrica M J Shahmoradgoli, Maria Zhang, Fan Ju, Zhenlin Liu, Wenbin Yang, Ji-Yeon Yoshihara, Kosuke Li, Jun Ling, Shiyun Seviour, Elena G Ram, Prahlad T Minna, John D Diao, Lixia Tong, Pan Heymach, John V Hill, Steven M Dondelinger, Frank Städler, Nicolas Byers, Lauren A Meric-Bernstam, Funda Weinstein, John N Broom, Bradley M Verhaak, Roeland G W Liang, Han Mukherjee, Sach Lu, Yiling Mills, Gordon B P30 CA016672/CA/NCI NIH HHS/United States P50 CA100632/CA/NCI NIH HHS/United States U54 CA112970/CA/NCI NIH HHS/United States TCGA CA143883/CA/NCI NIH HHS/United States U24 CA143883/CA/NCI NIH HHS/United States NCI P50CA70907/CA/NCI NIH HHS/United States MC_UP_1302/1/MRC_/Medical Research Council/United Kingdom P50 CA098258/CA/NCI NIH HHS/United States U01 CA168394/CA/NCI NIH HHS/United States P50 CA083639/CA/NCI NIH HHS/United States NCI U54 CA112970/CA/NCI NIH HHS/United States P50 CA070907/CA/NCI NIH HHS/United States U01 CA176284/CA/NCI NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't England 2014/05/30 Nat Commun. 2014 May 29;5:3887. doi: 10.1038/ncomms4887.","abstract":"Protein levels and function are poorly predicted by genomic and transcriptomic analysis of patient tumours. Therefore, direct study of the functional proteome has the potential to provide a wealth of information that complements and extends genomic, epigenomic and transcriptomic analysis in The Cancer Genome Atlas (TCGA) projects. Here we use reverse-phase protein arrays to analyse 3,467 patient samples from 11 TCGA 'Pan-Cancer' diseases, using 181 high-quality antibodies that target 128 total proteins and 53 post-translationally modified proteins. The resultant proteomic data are integrated with genomic and transcriptomic analyses of the same samples to identify commonalities, differences, emergent pathways and network biology within and across tumour lineages. In addition, tissue-specific signals are reduced computationally to enhance biomarker and target discovery spanning multiple tumour lineages. This integrative analysis, with an emphasis on pathways and potentially actionable proteins, provides a framework for determining the prognostic, predictive and therapeutic relevance of the functional proteome.","keywords":"Cluster Analysis Gene Dosage *Genome, Human Humans Neoplasm Proteins/genetics/*metabolism Neoplasms/*genetics Organ Specificity *Proteomics RNA, Messenger/genetics/metabolism Receptor, ErbB-2/genetics/metabolism Signal Transduction/genetics Statistics, Nonparametric","issn":"2041-1723","doi":"10.1038/ncomms4887","year":"2014","bibtex":"@article{RN6158,\n author = {Akbani, R. and Ng, P. K. and Werner, H. M. and Shahmoradgoli, M. and Zhang, F. and Ju, Z. and Liu, W. and Yang, J. Y. and Yoshihara, K. and Li, J. and Ling, S. and Seviour, E. G. and Ram, P. T. and Minna, J. D. and Diao, L. and Tong, P. and Heymach, J. V. and Hill, S. M. and Dondelinger, F. and Städler, N. and Byers, L. A. and Meric-Bernstam, F. and Weinstein, J. N. and Broom, B. M. and Verhaak, R. G. and Liang, H. and Mukherjee, S. and Lu, Y. and Mills, G. B.},\n title = {A pan-cancer proteomic perspective on The Cancer Genome Atlas},\n journal = {Nat Commun},\n volume = {5},\n pages = {3887},\n note = {2041-1723\nAkbani, Rehan\nNg, Patrick Kwok Shing\nWerner, Henrica M J\nShahmoradgoli, Maria\nZhang, Fan\nJu, Zhenlin\nLiu, Wenbin\nYang, Ji-Yeon\nYoshihara, Kosuke\nLi, Jun\nLing, Shiyun\nSeviour, Elena G\nRam, Prahlad T\nMinna, John D\nDiao, Lixia\nTong, Pan\nHeymach, John V\nHill, Steven M\nDondelinger, Frank\nStädler, Nicolas\nByers, Lauren A\nMeric-Bernstam, Funda\nWeinstein, John N\nBroom, Bradley M\nVerhaak, Roeland G W\nLiang, Han\nMukherjee, Sach\nLu, Yiling\nMills, Gordon B\nP30 CA016672/CA/NCI NIH HHS/United States\nP50 CA100632/CA/NCI NIH HHS/United States\nU54 CA112970/CA/NCI NIH HHS/United States\nTCGA CA143883/CA/NCI NIH HHS/United States\nU24 CA143883/CA/NCI NIH HHS/United States\nNCI P50CA70907/CA/NCI NIH HHS/United States\nMC_UP_1302/1/MRC_/Medical Research Council/United Kingdom\nP50 CA098258/CA/NCI NIH HHS/United States\nU01 CA168394/CA/NCI NIH HHS/United States\nP50 CA083639/CA/NCI NIH HHS/United States\nNCI U54 CA112970/CA/NCI NIH HHS/United States\nP50 CA070907/CA/NCI NIH HHS/United States\nU01 CA176284/CA/NCI NIH HHS/United States\nJournal Article\nResearch Support, N.I.H., Extramural\nResearch Support, Non-U.S. Gov't\nEngland\n2014/05/30\nNat Commun. 2014 May 29;5:3887. doi: 10.1038/ncomms4887.},\n abstract = {Protein levels and function are poorly predicted by genomic and transcriptomic analysis of patient tumours. Therefore, direct study of the functional proteome has the potential to provide a wealth of information that complements and extends genomic, epigenomic and transcriptomic analysis in The Cancer Genome Atlas (TCGA) projects. Here we use reverse-phase protein arrays to analyse 3,467 patient samples from 11 TCGA 'Pan-Cancer' diseases, using 181 high-quality antibodies that target 128 total proteins and 53 post-translationally modified proteins. The resultant proteomic data are integrated with genomic and transcriptomic analyses of the same samples to identify commonalities, differences, emergent pathways and network biology within and across tumour lineages. In addition, tissue-specific signals are reduced computationally to enhance biomarker and target discovery spanning multiple tumour lineages. 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