WormNet v3: A network-assisted hypothesis-generating server for Caenorhabditis elegans

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Cho, Ara ^a   Shin, Junha ^a   Hwang, Sohyun ^a,b   Kim, Chanyoung ^a   Shim, Hongseok ^a   Kim, Hyojin ^a   Kim, Hanhae ^a   Lee, Insuk ^a  

^a Yonsei University   (South Korea)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER INTERFACE; COMPUTER NETWORK; COMPUTER PREDICTION; COMPUTER SIMULATION; CONTEXT CENTRIC APPROACH; DATA ANALYSIS SOFTWARE; GENE CENTRIC APPROACH; GENE IDENTIFICATION; HYPOTHESIS; MICROBIAL GENE; NONHUMAN; PHENOTYPE; PHENOTYPE CENTRIC APPROACH; PRIORITY JOURNAL; RNA INTERFERENCE;

CAENORHABDITIS ELEGANS; METAZOA;

ANIMALS; CAENORHABDITIS ELEGANS; DICHLORVOS; GENE REGULATORY NETWORKS; GENES, HELMINTH; INSECTICIDES; INTERNET; PHENOTYPE; RNA INTERFERENCE; SOFTWARE;

EID: 84904798127     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku367     Document Type: Article

References (19)

1. Kaletta,T. and Hengartner,M.O. (2006) Finding function in novel targets: C. elegans as a model organism.Nat. Rev. Drug Discov., 5, 387-398.
2. Lee,I. (2013) Network approaches to the genetic dissection of phenotypes in animals and humans. Anim. Cells Syst., 17, 75-79.
3. Zhuang,J.J. and Hunter,C.P. (2012) RNA interference in Caenorhabditis elegans: uptake, mechanism, and regulation. Parasitology, 139, 560-573.
4. Mali,P., Esvelt,K.M. and Church,G.M. (2013) Cas9 as a versatile tool for engineering biology. Nat. Methods, 10, 957-963.
5. Ideker,T. and Sharan,R. (2008) Protein networks in disease. Genome Res., 18, 644-652.
6. Lehner,B. (2013) Genotype to phenotype: lessons from model organisms for human genetics. Nat. Rev. Genet., 14, 168-178.
7. Lee,I., Lehner,B., Crombie,C., Wong,W., Fraser,A.G. and Marcotte,E.M. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat. Genet., 40, 181-188.
8. Lee,I., Lehner,B., Vavouri,T., Shin,J., Fraser,A.G. and Marcotte,E.M. (2010) Predicting genetic modifier loci using functional gene networks. Genome Res., 20, 1143-1153.
9. Barrett,T., Wilhite,S.E., Ledoux,P., Evangelista,C., Kim,I.F., Tomashevsky,M.,Marshall,K.A., Phillippy,K.H., Sherman,P.M., Holko,M. et al.. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
10. Kim,E., Kim,H. and Lee,I. (2013) JiffyNet: a web-based instant protein network modeler for newly sequenced species. Nucleic Acids Res., 41, W192-W197.
11. Shin,J., Lee,T., Kim,H. and Lee,I. (2014) Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. Mol. Biosyst., 10, 24-29.
12. Kim,H., Shin,J., Kim,E., Kim,H., Hwang,S., Shim,J.E. and Lee,I. (2014) YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. Nucleic Acids Res., 42, D731-D736.
13. Yook,K., Harris,T.W., Bieri,T., Cabunoc,A., Chan,J., Chen,W.J., Davis,P., de la Cruz,N., Duong,A., Fang,R. et al.. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res., 40, D735-D741.
14. Hansen,M., Hsu,A.L., Dillin,A. and Kenyon,C. (2005) New genes tied to endocrine, metabolic, and dietary regulation of lifespan from a Caenorhabditis elegans genomic RNAi screen. PLoS Genet., 1, 119-128.
15. Hamilton,B., Dong,Y., Shindo,M., Liu,W., Odell,I., Ruvkun,G. and Lee,S.S. (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev., 19, 1544-1555.
16. Curran,S.P. and Ruvkun,G. (2007) Lifespan regulation by evolutionarily conserved genes essential for viability. PLoS Genet., 3, e56.
17. Lewis,J.A., Gehman,E.A., Baer,C.E. and Jackson,D.A. (2013) Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery. BMC Genomics, 14, 291.
18. Palmieri,F. (2008) Diseases caused by defects of mitochondrial carriers: a review. Biochim. Biophys. Acta, 1777, 564-578.
19. Leung,M.C., Williams,P.L., Benedetto,A., Au,C., Helmcke,K.J., Aschner,M. and Meyer,J.N. (2008) Caenorhabditis elegans: an emerging model in biomedical and environmental toxicology. Toxicol. Sci., 106, 5-28.