EvoCor: A platform for predicting functionally related genes using phylogenetic and expression profiles

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Dittmar, W James ^a   McIver, Lauren ^b   Michalak, Pawel ^b   Garner, Harold R ^b   Valdez, Gregorio ^a,c  

^a VIRGINIA TECH CARILION SCHOOL OF MEDICINE   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^c VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYOD1 PROTEIN; MYOGENIC FACTOR 5; MYOGENIN; TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; EVOCOR; EVOLUTION; GENE; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INSERTION; GENE ONTOLOGY; GENETIC DATABASE; HUMAN; MOUSE; MYF5 GENE; MYF6 GENE; MYOD1 GENE; MYOG GENE; NONHUMAN; ONLINE SYSTEM; PHYLOGENY; PRIORITY JOURNAL; PROTEIN INTERACTION; SEQUENCE HOMOLOGY; WEB BROWSER;

GENE EXPRESSION PROFILING; GENES; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; MARKOV CHAINS; PHYLOGENY; PROTEINS; SOFTWARE;

EID: 84904803906     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku442     Document Type: Article

References (20)

1. Lander,E.S. (2011) Initial impact of the sequencing of the human genome. Nature, 470, 187-197.
2. Pfeiffer,T. and Hoffmann,R. (2007) Temporal patterns of genes in scientific publications. Proc. Natl. Acad. Sci. U.S.A., 104, 12052-12056.
3. Pellegrini,M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles., Proc. Natl. Acad. Sci. U.S.A. 96, 4285-4288.
4. Bowers,P.M., Cokus,S.J., Eisenberg,D. and Yeates,T.O. (2004) Use of logic relationships to decipher protein network organization. Science (New York, N.Y.), 306, 2246-2249.
5. Barker,D. and Pagel,M. (2005) Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput. Biol., 1, e3.
6. Pagliarini,D.J., Calvo,S.E., Chang,B., Sheth,S.A., Vafai,S.B., Ong,S.-e.,Walford,G.A., Sugiana,C., Boneh,A., Chen,W.K. et al. (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell, 112-123.
7. Baughman,J.M., Perocchi,F., Girgis,H.S., Plovanich,M., Belcher-Timme,C.A., Sancak,Y., Bao,X.R., Strittmatter,L., Goldberger,O. and Bogorad,R.L. (2011) Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature, 476, 341-345.
8. Eddy,S.R. (2011)Accelerated Profile HMM Searches. PLoS Comput. Biol., 7, e1002195.
9. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
10. Su,A.I., Wiltshire,T., Batalov,S., Lapp,H., Ching,K.A., Block,D., Zhang,J., Soden,R., Hayakawa,M. and Kreiman,G. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A., 101, 6062-6067.
11. Lattin,J.E., Schroder,K., Su,A.I., Walker,J.R., Zhang,J., Wiltshire,T., Saijo,K., Glass,C.K., Hume,D.a., Kellie,S. et al. (2008) Expression analysis of G protein-coupled receptors in mouse macrophages. Immunome Res., 4, 5.
12. Langfelder,P. and Horvath,S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
13. Irizarry,R.A., Hobbs,B., Collin,F., Beazer-Barclay,Y.D., Antonellis,K.J., Scherf,U. and Speed,T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
14. Da Wei Huang,B.T.S. and Lempicki,R.A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
15. Yu,G., Li,F., Qin,Y., Bo,X., Wu,Y. and Wang,S. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics, 26, 976-978.
16. Bryson-Richardson,R.J. and Currie,P.D. (2008) The genetics of vertebrate myogenesis. Nat. Rev. Genet., 9, 632-646.
17. Seok,J., Warren,H.S., Cuenca,A.G., Mindrinos,M.N., Baker,H.V., Xu,W., Richards,D.R.,McDonald-Smith,G.P., Gao,H. and Hennessy,L. (2013) Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc. Natl. Acad. Sci. U.S.A., 110, 3507-3512.
18. Mellor,J.C., Yanai,I., Clodfelter,K.H.,Mintseris,J. and Delisi,C. (2002) Predictome : a database of putative functional links between proteins. Nucleic Acids Res., 30, 306-309.
19. Lee,I., Blom,U.M., Wang,P.I., Shim,J.E. and Marcotte,E.M. (2011) Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res., 21, 1109-1121.
20. Franceschini,A., Szklarczyk,D., Frankild,S., Kuhn,M., Simonovic,M., Roth,A., Lin,J., Minguez,P., Bork,P. and von Mering,C. (2013) STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.