Network analysis of reverse phase protein expression data: Characterizing protein signatures in acute myeloid leukemia cytogenetic categories t(8;21) and inv(16)

Proteomics

Volumn 12, Issue 13, 2012, Pages 2084-2093

  York, Heather ^a   Kornblau, Steven M ^b   Qutub, Amina Ann ^a  

^a Rice University   (United States)

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

Author keywords

AML; Cytogenetics; Network analysis; Protein signatures; RPPA; Systems biology

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; CD4+ T LYMPHOCYTE; COMPUTER ANALYSIS; CONTROLLED STUDY; CYTOGENETICS; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION;

CHROMOSOME ABERRATIONS; CYTOGENETIC ANALYSIS; HUMANS; LEUKEMIA, MYELOID, ACUTE; ONCOGENE PROTEINS, FUSION; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEINS; PROTEOMICS; REGRESSION ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTOME;

EID: 84864024038     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100491     Document Type: Article

References (14)

1. Kornblau, S. M., Tibes, R., Qiu, Y. H., Chen, W. et al., Functional proteomic profiling of AML predicts response and survival. Blood 2009, 113, 154-164.
2. Tibes, R., Qiu, Y., Lu, Y., Hennessy, B. et al., 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. 2006, 5, 2512-2521.
3. Yasar, D., Karadogan, I., Alanoglu, G., Akkaya, B. et al., Array comparative genomic hybridization analysis of adult acute leukemia patients. Cancer Genet. Cytogenet. 2010, 197, 122-129.
4. Deneberg, S., Grovdal, M., Karimi, M., Jansson, M. et al., Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia 2010, 24, 932-941.
5. Marcucci, G., Maharry, K., Radmacher, M. D., Mrozek, K. et al., Prognostic significance of, and gene and microRNA expression signatures associated with, CEBPA mutations in cytogenetically normal acute myeloid leukemia with high-risk molecular features: a Cancer and Leukemia Group B Study. J. Clin. Oncol. 2008, 26, 5078-5087.
6. Friedman, J., Hastie, T., Tibshirani, R., Applications of the lasso and grouped lasso to the estimation of sparse graphical models. Technical Reports, Available Online: Stanford University, 2010.
7. Meinshausen, N., Buhlmann, P., High dimensional graphs and variable selection with the lasso. Ann. Stat. 2006, 34, 1-32.
8. Tibshirani, R., Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Ser. B 1996, 58, 267-288.
9. Friedman, J., Hastie, T., Tibshirani, R., Sparse inverse covariance estimation with the graphical lasso. Biostatistics 2008, 9, 432-441.
10. Gradshteyn, I. S., Ryzhik, I. M., Tables of Integrals, Series, and Products, 6th Ed., Academic Press, San Diego 2000, pp. 1114-1125.
11. Tarcea, V. G., Weymouth, T., Ade, A., Bookvich, A. et al., Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res. 2009, 37, D642-D646.
12. Gao, J., Ade, A. S., Tarcea, V. G., Weymouth, T. E. et al., Integrating and annotating the interactome using the MiMI plugin for cytoscape. Bioinformatics 2009, 25, 137-138.
13. Assenov, Y., Ramirez, F., Schelhorn, S. E., Lengauer, T. et al., Computing topological parameters of biological networks. Bioinformatics 2008, 24, 282-284.
14. Kornblau, S. M., Qiu, Y. H., Zhang, N., Singh, N. et al., Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia. Blood 2011, 118, 5604-5612.