Predicting potential cancer genes by integrating network properties, sequence features and functional annotations

Science China Life Sciences

Volumn 56, Issue 8, 2013, Pages 751-757

  Liu, Wei ^a   Xie, HongWei ^a  

^a NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

Author keywords

cancer gene; functional annotation; logistic regression; network property; sequence feature

Indexed keywords

EID: 84881256734     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-013-4500-6     Document Type: Article

References (26)

1. Vogelstein B, Kinzler K W. Cancer genes and the pathways they control. Nat Med, 2004, 10: 789-799.
2. Futreal P A, Coin L, Marshall M, et al. A census of human cancer genes. Nat Rev Cancer, 2004, 4: 177-183.
3. Strausberg R L, Simpson A J, Wooster R. Sequence-based cancer genomics: progress, lessons and opportunities. Nat Rev Genet, 2003, 4: 409-418.
4. Altshuler D, Daly M J, Lander E S. Genetic mapping in human disease. Science, 2008, 322: 881-888.
5. Aragues R, Sander C, Oliva B. Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics, 2008, 9: 172.
6. Furney S J, Higgins D G, Ouzounis C A, et al. Structural and functional properties of genes involved in human cancer. BMC Genomics, 2006, 7: 3.
7. Ostlund G, Lindskog M, Sonnhammer E L. Network-based Identification of novel cancer genes. Mol Cell Proteomics, 2010, 9: 648-655.
8. Li L, Zhang K, Lee J, et al. Discovering cancer genes by integrating network and functional properties. BMC Med Genomics, 2009, 2: 61.
9. Wang E, Lenferink A, O'Connor-McCourt M. Cancer systems biology: exploring cancer-associated genes on cellular networks. Cell Mol Life Sci, 2007, 64: 1752-1762.
10. Milenkovic T, Memisevic V, Ganesan A K, et al. Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J R Soc, 2010, 7: 423-437.
11. Brown K R, Jurisica I. Online predicted human interaction database. Bioinformatics, 2005, 21: 2076-2082.
12. Alfarano C, Andrade C E, Anthony K, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res, 2005, 33: D418-D424.
13. Peri S, Navarro J D, Kristiansen T Z, et al. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res, 2004, 32: D497-D501.
14. Chatr-aryamontri A, Ceol A, Palazzi L M, et al. MINT: the Molecular INTeraction database. Nucleic Acids Res, 2007, 35: D572-D574.
15. Cui Q, Ma Y, Jaramillo M, et al. A map of human cancer signaling. Mol Syst Biol, 2007, 3: 152.
16. Hamosh A, Scott A F, Amberger J S, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res, 2005, 33: D514-D517.
17. D'Antonio M, Pendino V, Sinha S, et al. Network of Cancer Genes (NCG 3. 0): integration and analysis of genetic and network properties of cancer genes. Nucleic Acids Res, 2012, 40: D978-D983.
18. Maglott D, Ostell J, Pruitt K D, et al. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res, 2007, 35: D26-D31.
19. Tu Z, Wang L, Xu M, et al. Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics, 2006, 7: 31.
20. Frank E, Hall M, Trigg L, et al. Data mining in bioinformatics using Weka. Bioinformatics, 2004, 20: 2479-2481.
21. Hanley J A, McNeil B J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 1982, 143: 29-36.
22. Xu J, Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics, 2006, 22: 2800-2805.
23. Kyte J, Doolittle R F. A simple method for displaying the hydropathic character of a protein. J Mol Biol, 1982, 157: 105-132.
24. Bakheet T M, Doig A J. Properties and identification of human protein drug targets. Bioinformatics, 2009, 25: 451-457.
25. Harris M A, Clark J, Ireland A, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res, 2004, 32: D258-D261.
26. Huang da W, Sherman B T, Lempicki R A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res, 2009, 37: 1-13.