From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction

FEBS Letters

Volumn 584, Issue 16, 2010, Pages 3635-3643

  Zhang, Shi Hua ^a   Wu, Chao ^a   Li, Xia ^a   Chen, Xi ^a   Jiang, Wei ^a   Gong, Bin Sheng ^a   Li, Jiang ^a   Yan, Yu Qing ^b  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Disease phenotype; Gene functional module; Genetic origin; Phenotype network; Text mining

Indexed keywords

GENE PRODUCT;

ARTICLE; BONE DISEASE; CARDIOVASCULAR DISEASE; DEVELOPMENTAL DISORDER; ENDOCRINE DISEASE; EYE DISEASE; GENE CLUSTER; GENE FUNCTION; GENE INTERACTION; GENE MAPPING; GENE VECTOR; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC SIMILARITY; HUMAN; METABOLIC DISORDER; MUSCLE DISEASE; NEUROLOGIC DISEASE; PATHOPHYSIOLOGY; PHENOTYPE; PRIORITY JOURNAL; SCORING SYSTEM; SKIN DISEASE;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DISEASE; GENE REGULATORY NETWORKS; HUMANS; PHENOTYPE;

EID: 77955663914     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.07.038     Document Type: Article

References (32)

1. Kuttenkeuler D., Boutros M. Genome-wide RNAi as a route to gene function in Drosophila. Brief Funct. Genomic Proteomic 2004, 3:168-176.
2. Giaever G., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391.
3. Rual J.F., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 2004, 14:2162-2168.
4. Shi Y. Mammalian RNAi for the masses. Trends Genet. 2003, 19:9-12.
5. Hamosh A., Scott A.F., Amberger J., Bocchini C., Valle D., McKusick V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2002, 30:52-55.
6. Freudenberg J., Propping P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 2002, 18(Suppl. 2):S110-S115.
7. van Driel M.A., Bruggeman J., Vriend G., Brunner H.G., Leunissen J.A. A text-mining analysis of the human phenome. Eur. J. Hum. Genet. 2006, 14:535-542.
8. Badano J.L., Katsanis N. Beyond Mendel: an evolving view of human genetic disease transmission. Nat. Rev. Genet. 2002, 3:779-789.
9. Gandhi T.K., et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 2006, 38:285-293.
10. Kann M.G. Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform. 2007, 8:333-346.
11. Blake, J.A. and Harris, M.A. (2002) The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr. Protocol Bioinformatics, Chapter 7, Unit 72.
12. Aronson A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp. 2001, 17-21.
13. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004, 32:D267-D270.
14. Wilbur W.J., Yang Y. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Med. 1996, 26:209-222.
15. Bader G.D., et al. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2.
16. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4:P3.
17. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., Barabasi A.L. The human disease network. Proc. Natl. Acad. Sci. USA 2007, 104:8685-8690.
18. Park J., Barabasi A.L. Distribution of node characteristics in complex networks. Proc. Natl. Acad. Sci. USA 2007, 104:17916-17920.
19. Barabasi A.L., Bonabeau E. Scale-free networks. Sci. Am. 2003, 288:60-69.
20. Gong Y., Zhang Z. Global robustness and identifiability of random, scale-free, and small-world networks. Ann. NY. Acad. Sci. 2009, 1158:82-92.
21. Peri S., et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003, 13:2363-2371.
22. Jiang, J.J. and Conrath, D.W. (1997) Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy. ROCLING X.9008.
23. Guo X., Liu R., Shriver C.D., Hu H., Liebman M.N. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22:967-973.
24. Frohlich H., Speer N., Poustka A., Beissbarth T. GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 2007, 8:166.
25. Lee D.S., Park J., Kay K.A., Christakis N.A., Oltvai Z.N., Barabasi A.L. The implications of human metabolic network topology for disease comorbidity. Proc. Natl. Acad. Sci. USA 2008, 105:9880-9885.
26. Chen J., Yuan B. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 2006, 22:2283-2290.
27. Hwang W., Cho Y.R., Zhang A., Ramanathan M. A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol. Biol. 2006, 1:24.
28. Luo F., Yang Y., Chen C.F., Chang R., Zhou J., Scheuermann R.H. Modular organization of protein interaction networks. Bioinformatics 2007, 23:207-214.
29. Ulitsky I., Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 2007, 1:8.
30. Brown K.R., Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21:2076-2082.
31. Rual J.F., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178.
32. Stelzl U., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968.