Ontological discovery environment: A system for integrating gene-phenotype associations

Genomics

Volumn 94, Issue 6, 2009, Pages 377-387

  Baker, Erich J ^a   Jay, Jeremy J ^b   Philip, Vivek M ^c   Zhang, Yun ^b   Li, Zuopan ^b   Kirova, Roumyana ^d   Langston, Michael A ^b,d   Chesler, Elissa J ^d  

^a Baylor University   (United States)

^b University of Tennessee Knoxville   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Combinatorial algorithms; Homology; Microarray; Ontology

Indexed keywords

ALCOHOLISM; ARTICLE; COMPUTER PROGRAM; DNA MICROARRAY; EXPERIMENTAL MODEL; GENE EXPRESSION; GENE FUNCTION; GENE LIBRARY; GENETIC ALGORITHM; GENETIC DATABASE; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; INTERNET; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; SPECIES IDENTIFICATION; STATISTICAL MODEL;

ALCOHOLISM; ANIMALS; BRAIN INJURIES; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE REGULATORY NETWORKS; GENOMICS; GENOTYPE; HUMANS; INTERNET; INVERTEBRATES; MENTAL DISORDERS; MICE; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI; RATS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; USER-COMPUTER INTERFACE; VERTEBRATES;

EID: 70449134639     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.08.016     Document Type: Article

References (43)

1. Smith C.L., Goldsmith C.A., and Eppig J.T. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 6 1 (2005) R7
2. Gkoutos G.V., Green E.C., Mallon A.M., Hancock J.M., and Davidson D. Building mouse phenotype ontologies. Pac. Symp. Biocomput. (2004) 178-189
3. Ashburner M., Ball C.A., Blake J.A.B.D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
4. Kanehisa M., and Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 1 (2000) 27-30
5. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C., and Conklin B.R. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31 1 (2002) 19-20
6. Hosack D.A., Dennis Jr. G., Sherman B.T., Lane H.C., and Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol. 4 10 (2003) R70
7. Lee H.K., Braynen W., Keshav K., Pavlidis P., and Ermine J. Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6 1 (2005) 269
8. Liu H., Hu Z.Z., and Wu C.H. DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics 6 (2005) 201
9. Zhang B., Schmoyer D., Kirov S., and Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5 1 (2004) 16
10. Le-Niculescu H., McFarland M.J., Mamidipalli S., Ogden C.A., Kuczenski R., Kurian S.M., Salomon D.R., Tsuang M.T., Nurnberger Jr. J.I., and Niculescu A.B. Convergent functional genomics of bipolar disorder: from animal model pharmacogenomics to human genetics and biomarkers. Neurosci. Biobehav. Rev. 31 6 (2007) 897-903
11. Bogue M.A., Grubb S.C., Maddatu T.P., and Bult C.J. Mouse Phenome Database (MPD). Nucleic Acids Res 35 Database issue (2007) D643-D649
12. Fernandez-Ricaud L., Warringer J., Ericson E., Glaab K., Davidsson P., Nilsson F., Kemp G.J., Nerman O., and Blomberg A. PROPHECY-a yeast phenome database, update 2006. Nucleic Acids Res. 35 Database issue (2007) D463-D467
13. Masuya H., Yoshikawa S., Heida N., Toyoda T., Wakana S., and Shiroishi T. Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice. J. Bioinform. Comput. Biol. 5 6 (2007) 1173-1191
14. Muilu J., Peltonen L., and Litton J.E. The federated database-a basis for biobank-based post-genome studies, integrating phenome and genome data from 600,000 twin pairs in Europe. Eur. J. Hum. Genet. 15 7 (2007) 718-723
15. Toyoda T., Mochizuki Y., Player K., Heida N., Kobayashi N., and Sakaki Y. OmicBrowse: a browser of multidimensional omics annotations. Bioinformatics 23 4 (2007) 524-526
16. van Driel M.A., Bruggeman J., Vriend G., Brunner H.G., and Leunissen J.A. A text-mining analysis of the human phenome. Eur. J. Hum. Genet. 14 5 (2006) 535-542
17. Kim W.K., Krumpelman C., and Marcotte E.M. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol. 9 Suppl. 1 (2008) S5
18. Pena-Castillo L., Tasan M., Myers C.L., Lee H., Joshi T., Zhang C., Guan Y., Leone M., Pagnani A., Kim W.K., et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 9 Suppl. 1 (2008) S2
19. Li J., Li X., Su H., Chen H., and Galbraith D.W. A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana. Bioinformatics 22 16 (2006) 2037-2043
20. Oti M., Huynen M.A., and Brunner H.G. Phenome connections. Trends Genet. 24 3 (2008) 103-106
21. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., and Barabasi A.L. The human disease network. Proc. Natl. Acad. Sci. U. S. A. 104 21 (2007) 8685-8690
22. Downey R.G., and Fellows M.R. Parameterized Complexity (1999), Springer, Verlag
23. Zhang Y., Abu-Khzam F.N., Baldwin N.E., Chesler E.J., Langston M.A., and Samatova N.F. Genome-scale computational approaches to memory-intensive applications in systems biology. Super Computing (2005)
24. Mulligan M.K., Ponomarev I., Hitzemann R.J., Belknap J.K., Tabakoff B., Harris R.A., Crabbe J.C., Blednov Y.A., Grahame N.J., Phillips T.J., et al. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc. Natl. Acad. Sci. U. S. A. 103 16 (2006) 6368-6373
25. Kerns R.T., Ravindranathan A., Hassan S., Cage M.P., York T., Sikela J.M., Williams R.W., and Miles M.F. Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. J. Neurosci. 25 9 (2005) 2255-2266
26. Matzilevich D.A., Rall J.M., Moore A.N., Grill R.J., and Dash P.K. High-density microarray analysis of hippocampal gene expression following experimental brain injury. J. Neurosci. Res. 67 5 (2002) 646-663
27. Mitkus S.N., Hyde T.M., Vakkalanka R., Kolachana B., Weinberger D.R., Kleinman J.E., and Lipska B.K. Expression of oligodendrocyte-associated genes in dorsolateral prefrontal cortex of patients with schizophrenia. Schizophr. Res. 98 1-3 (2008) 129-138
28. Balasubramanian R., LaFramboise T., Scholtens D., and Gentleman R. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics 20 18 (2004) 3353-3362
29. Marquet G., Mosser J., and Burgun A. A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: the case of OBO disease ontologies. Int. J. Med. Inform. 76 Suppl. 3 (2007) S353-S361
30. Su A.I., Cooke M.P., Ching K.A., Hakak Y., Walker J.R., Wiltshire T., Orth A.P., Vega R.G., Sapinoso L.M., Moqrich A., et al. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. U. S. A. 99 7 (2002) 4465-4470
31. Chesler E.J., Wang J., Lu L., Qu Y., Manly K.F., and Williams R.W. Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypes. Neuroinformatics 1 4 (2003) 343-357
32. Blaschke C., and Valencia A. Automatic ontology construction from the literature. Genome Inform. Ser. Workshop Genome Inform. 13 (2002) 201-213
33. Homayouni R., Heinrich K., Wei L., and Berry M.W. Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 21 1 (2005) 104-115
34. Belfer I., Wu T., Kingman A., Krishnaraju R.K., Goldman D., and Max M.B. Candidate gene studies of human pain mechanisms: methods for optimizing choice of polymorphisms and sample size. Anesthesiology 100 6 (2004) 1562-1572
35. Maxson S.C. Searching for candidate genes with effects on an agonistic behavior, offense, in mice. Behav. Genet. 26 5 (1996) 471-476
36. Kreek M.J., Nielsen D.A., and LaForge K.S. Genes associated with addiction: alcoholism, opiate, and cocaine addiction. Neuromol. Med. 5 1 (2004) 85-108
37. Bare J.C., Shannon P.T., Schmid A.K., and Baliga N.S. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics 8 (2007) 456
38. Sherman B.T., Huang da W., Tan Q., Guo Y., Bour S., Liu D., Stephens R., Baseler M.W., Lane H.C., and Lempicki R.A. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 8 (2007) 426
39. Jensen L.J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M., et al. STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37 Database issue (2009) D412-D416
40. Smith B., Ashburner M., Rosse C., Bard J., Bug W., Ceusters W., Goldberg L.J., Eilbeck K., Ireland A., Mungall C.J., et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25 11 (2007) 1251-1255
41. Fielding R.T., and Kaiser G. The Apache HTTP Server Project. IEEE Internet Computing 1 4 (1997) 88-90
42. Zhang Y, Chesler E, Langston M: On finding bicliques in bipartite graphs: a novel algorithm with application to the integration of diverse biological data types. In: HICSS: 2008; Big Island, Hawaii; 2008.
43. Barabasi A.L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5 2 (2004) 101-113