The network organization of cancer-associated protein complexes in human tissues

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Zhao, Jing ^a   Lee, Sang Hoon ^b,c   Huss, Mikael ^d,e   Holme, Petter ^b,f  

^a ARMY ENGINEERING UNIVERSITY OF PLA   (China)

^b UMEÅ UNIVERSITY   (Sweden)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d SCIENCE FOR LIFE LABORATORY   (Sweden)

^e STOCKHOLM UNIVERSITY   (Sweden)

^f Sungkyunkwan University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; BRAIN TUMOR; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; NEOPLASM; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REPRODUCIBILITY;

ALGORITHMS; BRAIN NEOPLASMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MODELS, BIOLOGICAL; MULTIPROTEIN COMPLEXES; NEOPLASMS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84890066246     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01583     Document Type: Article

References (51)

1. Mohammadi, A., Saraee, M. & Salehi, M. Identification of disease-causing genes using microarray data mining and Gene Ontology. BMC Medical Genomics 4, 12 (2011).
2. Ruan, X., Wang, J., Li, H., Perozzi, R. E. & Perozzi, E. F. The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data. Journal of Biomedical Informatics 41, 530-543 (2008).
3. Nitsch, D. et al. Network Analysis of Differential Expression for the Identification of Disease-Causing Genes. PLoS ONE 4, e5526 (2009).
4. Zhao, J., Yang, T.-H., Huang, Y. & Holme, P. Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach. PLoS ONE 6, e24306 (2011).
5. Wu, X., Jiang, R., Zhang, M. Q. & Li, S. Network-based global inference of human disease genes. Molecular Systems Biology 4, 189 (2008).
6. Yao, X., Hao, H., Li, Y. & Li, S. Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. BMC Systems Biology 5, 79 (2011).
7. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
8. Ito, T. et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 97, 1143-7 (2000).
9. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences 98, 4569-4574 (2001).
10. Yu, H. et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science 322, 104-110 (2008).
11. Puig, O. et al. The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification. Methods 24, 218-229 (2001).
12. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotech 17, 1030-1032 (1999).
13. Gavin, A.-C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
14. Krogan, N. J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
15. Lee, S. H., Kim, P.-J. & Jeong, H. Global organization of protein complexome in the yeast Saccharomyces cerevisiae. BMC Syst Biol 5, 126 (2011).
16. Parsons, D. W. et al. An Integrated Genomic Analysis of Human Glioblastoma Multiforme. Science 321, 1807-1812 (2008).
17. Jones, S. et al. Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses. Science 321, 1801-1806 (2008).
18. Hwang, S. et al. A protein interaction network associated with asthma. Journal of Theoretical Biology 252, 722-731 (2008).
19. Qiu, Y.-Q., Zhang, S., Zhang, X.-S. & Chen, L. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics 11, 26 (2010).
20. Suthram, S. et al. Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. PLoS Computational Biology 6, e1000662 (2010).
21. Zhao, J., Chen, J., Yang, T.-H. & Holme, P. Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis. BMC Systems Biology 6, S4 (2012).
22. Liu, K.-Q., Liu, Z.-P., Hao, J.-K., Chen, L. & Zhao, X.-M. Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics 13, 126 (2012).
23. Bossi, A. & Lehner, B. Tissue specificity and the human protein interaction network. Mol Syst Biol 5, 260 (2009).
24. Liang, S., Li, Y., Be, X., Howes, S. & Liu, W. Detecting and profiling tissue-selective genes. Physiol Genomics 26, 158-162 (2006).
25. Axelsen, J., Lotem, J., Sachs, L. & Domany, E. Genes overexpressed in different human solid cancersexhibit different tissue-specific expression profiles. Proc Natl Acad Sci U S A 104, 13122-13127 (2007).
26. Wang, L., Srivastava, A. & Schwartz, C. Microarray data integration for genomewideanalysis of human tissue-selective geneexpression. BMC Genomics 11, S15 (2010).
27. Chang, C. et al. Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis. PLoS ONE 6, e22859 (2011).
28. Liu, X., Yu, X., Zack, D., Zhu, H. & Qian, J. TiGER: A database for tissue-specific gene expression and regulation. BMC Bioinformatics 9, 271 (2008).
29. Wang, L., Srivastava, A. & Schwartz, C. Microarray data integration for genomewide analysis of human tissue-selective gene expression. BMC Genomics 11, S15 (2010).
30. Lage, K. et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotech 25, 309-316 (2007).
31. Lage, K. et al. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A 105, 20870-20875 (2008).
32. Lukk, M. et al. A global map of human gene expression. Nat Biotechnol 28, 322-324 (2010).
33. Ruepp, A. et al. CORUM: the comprehensive resource of mammalian protein complexes 2009. Nucleic Acids Research 38, D497-D501 (2010).
34. Ruepp, A. et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research 32, 5539-5545 (2004).
35. Parham, P. The Immune System (Garland Science, New York, 2009).
36. Safran, M. et al. GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18, 1542-1543 (2002).
37. Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological) 57, 289-300 (1995).
38. Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550 (2005).
39. Lotem, J., Netanely, D., Domany, E. & Sachs, L. Human cancers overexpress genes that are specific to a variety of normal human tissues. Proceedings of the National Academy of Sciences of the United States of America 102, 18556-18561 (2005).
40. Lee, S. H., Kim, P.-J., Ahn, Y.-Y. & Jeong, H. Googling Social Interactions: Web Search Engine Based Social Network Construction. PLoS ONE 5, e11233 (2010).
41. Ward, J. Hierarchical grouping to optimize an objective function. J. Amer. Statist. Assoc. 58, 236-244 (1963).
42. Lance, G. & Williams, W. A general theory of classificatory sorting strategies. Comput J 9, 373-380 (1967).
43. Rogers, F. Medical subject headings. Bull Med Libr AssocBull Med Libr Assoc 5151, 114-116 (1963).
44. Doms, A. & Schroeder, M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Research 33, W783-W786 (2005).
45. Holme, P. Model validation of simple-graph representation of metabolism. J. Roy. Soc. Interface 40, 1027-1034 (2009).
46. Zhao, J. et al. Reconstruction and Analysis of Human Liver-Specific Metabolic Network Based on CNHLPP Data. Journal of Proteome Research 9, 1648-1658 (2010).
47. Irizarry, R. A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
48. Ponten, F. et al. A global view of protein expression in human cells, tissues, and organs. Molecular Systems Biology 5, 337 (2009).
49. Huttlin, E. L. et al. A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression. Cell 143, 1174-1189 (2010).
50. Lu, P., Vogel, C., Wang, R., Yao, X. & Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotech 25, 117-124 (2007).
51. Schwanhausser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).