Inferring gene ontologies from pairwise similarity data

Bioinformatics

Volumn 30, Issue 12, 2014, Pages

  Kramer, Michael ^a   Dutkowski, Janusz ^a   Yu, Michael ^a   Bafna, Vineet ^b   Ideker, Trey ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETICS; GENOMICS; METHODOLOGY; SEMANTICS; YEAST;

ALGORITHMS; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENE REGULATORY NETWORKS; GENOMICS; SEMANTICS; YEASTS;

EID: 84902463000     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu282     Document Type: Article

References (27)

1. Ahn, Y.Y. et al. (2010) Link communities reveal multiscale complexity in networks. Nature, 466, 761-764.
2. Alterovitz, G. et al. (2010) Ontology engineering. Nat. Biotechnol., 28, 128-130.
3. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
4. Becker, E. et al. (2012) Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics, 28, 84-90.
5. Carvunis, A. and Ideker, T. (2014) Siri of the cell: what biology could learn from the iPhone. Cell, 157, 534-538.
6. Chiba, N. and Nishizeki, T. (1985) Arboricity and subgraph listing algorithms. SIAM J. Comput., 14, 210-223.
7. Costanzo, M. et al. (2010) The genetic landscape of a cell. Science, 327, 425-431.
8. Dolinski, K. and Botstein, D. (2013) Automating the construction of gene ontologies. Nat. Biotechnol., 31, 34-35.
9. Dutkowski, J. et al. (2013) A gene ontology inferred from molecular networks. Nat. Biotechnol., 31, 38-45.
10. Florek, K. et al. (1951) Sur la liaison et la division des points d'un ensemble fini. Colloq. Math., 2, 282-285.
11. Gene Ontology Consortium. (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
12. Holmans, P. et al. (2009) Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am. J. Hum. Genet., 85, 13-24.
13. Hubble, J. et al. (2009) Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res., 37, D898-D901.
14. Kim, H. et al. (2014) YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. Nucleic Acids Res., 42, D731-D736.
15. Kovacs, I.A. et al. (2010) Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS One, 5, e12528+.
16. Kumpula, J.M. et al. (2008) Sequential algorithm for fast clique percolation. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 78, 026109.
17. Lancichinetti, A. et al. (2009) Detecting the overlapping and hierarchical community structure in complex networks. New J. Phys., 11, 033015.
18. Park, Y. and Bader, J.S. (2011) Resolving the structure of interactomes with hierarchical agglomerative clustering. BMC Bioinformatics, 12 (Suppl. 1), S44.
19. Pena-Castillo, L. et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol., 9 (Suppl. 1), S2.
20. Resnik, P. (1995) Using information content to evaluate semantic similarity in a taxonomy. Int. Joint Conf. Artif., 1, 448-453.
21. Sales-Pardo, M. et al. (2007) Extracting the hierarchical organization of complex systems. Proc. Natl Acad. Sci. USA, 104, 15224-15229.
22. Sneath, P.H. and Sokal, R.R. (1973) Numerical Taxonomy. The Principles and Practice of Numerical Classification. W. H. Freeman, San Francisco, USA.
23. Sokal, R.R. and Michener, C.D. (1958) A statistical method for evaluating systematic relationships. The University of Kansas Scientific Bulletin, 38, 1409-1438.
24. Sørensen, T. (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Biol. Skr., 5, 1-34.
25. Wang, K. et al. (2010) Analysing biological pathways in genome-wide association studies. Nat. Rev. Genet., 11, 843-854.
26. Ward, J.H. (1963) Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc., 58, 236-244.
27. Yan, H. et al. (2010) A genome-wide gene function prediction resource for Drosophila melanogaster. PLoS One, 5, e12139.