Development of a robust classifier for quality control of reverse-phase protein arrays

Bioinformatics

Volumn 31, Issue 6, 2015, Pages 912-918

  Ju, Zhenlin ^a   Liu, Wenbin ^a   Roebuck, Paul L ^a   Siwak, Doris R ^a   Zhang, Nianxiang ^a   Lu, Yiling ^a   Davies, Michael A ^a   Akbani, Rehan ^a   Weinstein, John N ^a   Mills, Gordon B ^a   Coombes, Kevin R ^a,b  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; PROCEDURES; PROTEIN MICROARRAY; PROTEOMICS; QUALITY CONTROL; SOFTWARE;

ALGORITHMS; PROTEIN ARRAY ANALYSIS; PROTEOMICS; QUALITY CONTROL; SOFTWARE;

EID: 84925269960     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu736     Document Type: Article

References (20)

1. Akaike, H. (1974) A new look at the statistical model identification. IEEE Trans. Automat. Cont., 19, 716-723.
2. Akbani, R. et al. (2014) A pan-cancer proteomic perspective on the cancer genome atlas. Nat. Commun., 5, 3887.
3. Cancer Genome Atlas Network. (2012a) Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487, 330-337.
4. Cancer Genome Atlas Network. (2012b) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
5. Cancer Genome Atlas Research Network et al. (2013) Integrated genomic characterization of endometrial carcinoma. Nature, 497, 67-73.
6. Carey, M.S. et al. (2010) Functional proteomic analysis of advanced serous ovarian cancer using reverse phase protein array: TGF-beta pathway signaling indicates response to primary chemotherapy. Clin. Cancer Res., 16, 2852-2860.
7. Chen, Y. et al. (2011) Combined Src and ER blockade impairs human breast cancer proliferation in vitro and in vivo. Breast Cancer Res. Treat., 128, 69-78.
8. Cohen, J. (1968) Weighted kappa: nominal scale agreement with provision for scaled disagreement or partial credit. Psychol. Bull., 70, 213-220.
9. Davies, M.A. et al. (2009) Integrated molecular and clinical analysis of AKT activation in metastatic melanoma. Clin. Cancer Res., 15, 7538-7546.
10. Dobson, A.J. and Barnett, A.G. (2008) Introduction to Generalized Linear Models, 3rd edn. Chapman and Hall, Boca Raton, FL.
11. Grote, T. et al. (2008) Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer. Proteomics, 8, 3051-3060.
12. Hardin, J. and Hilbe, J. (2007) Generalized Linear Models and Extensions, 2nd edn. Stata Press, College Station, TX.
13. Hendricks, W.A. and Robey, K.W. (1936) The sampling distribution of the coefficient of variation. Ann. Math. Stat., 7, 129-132.
14. Liang, H. et al. (2012) Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res., 22, 2120-2129.
15. Nishizuka, S. et al. (2003) Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl. Acad. Sci. USA., 100, 14229-14234.
16. Park, E.S. et al. (2010) Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set. Mol. Cancer Ther., 9, 257-267.
17. Paweletz, C.P. et al. (2001) Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene, 20, 1981-1989.
18. Tibes, R. et al. (2006) Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther., 5, 2512-2521.
19. Tsao, T. et al. (2010) Role of peroxisome proliferator-activated receptorgamma and its coactivator DRIP205 in cellular responses to CDDO (RTA-401) in acute myelogenous leukemia. Cancer Res., 70, 4949-4960.
20. Yang, J.Y. et al. (2013) Predicting time to ovarian carcinoma recurrence using protein markers. J. Clin. Invest., 123, 3740-3750.