MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D848-D854

  Kim, Eiru ^a   Hwang, Sohyun ^a,b   Kim, Hyojin ^a   Shim, Hongseok ^a   Kang, Byunghee ^a   Yang, Sunmo ^a   Shim, Jae Ho ^a   Shin, Seung Yeon ^a   Marcotte, Edward M ^b   Lee, Insuk ^a  

^a Yonsei University   (South Korea)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; GENE FUNCTION; GENE IDENTIFICATION; GENETIC DATABASE; GENOMICS; INFORMATION SERVICE; MOUSENET DATABASE; MUS MUSCULUS; NONHUMAN; PRIORITY JOURNAL; VERTEBRATE; ANIMAL; BOVINE; DISEASES; DOG; GENE REGULATORY NETWORK; GENETICS; HUMAN; MOUSE; PHENOTYPE; RAT;

ANIMALS; CATTLE; DATABASES, GENETIC; DISEASE; DOGS; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; MICE; PHENOTYPE; RATS;

EID: 84976870544     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1155     Document Type: Article

References (31)

1. Blake, J. A., Christie, K. R., Dolan, M. E., Drabkin, H. J., Hill, D. P., Ni, L., Sitnikov, D., Burgess, S., Buza, T., Gresham, C. et al. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
2. Kim, W. K., Krumpelman, C. and Marcotte, E. M. (2008) Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol., 9, S5.
3. Pena-Castillo, L., Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y. F., Leone, M., Pagnani, A., Kim, W. K. et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol., 9, S2.
4. 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.
5. Blake, J. A., Bult, C. J., Eppig, J. T., Kadin, J. A., Richardson, J. E. and Grp, M. G. D. (2014) The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. Nucleic Acids Res., 42, D810-D817.
6. Cho, A., Shin, J., Hwang, S., Kim, C., Shim, H., Kim, H., Kim, H. and Lee, I. (2014) WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans. Nucleic Acids Res., 42, W76-W82.
7. Shin, J., Yang, S., Kim, E., Kim, C. Y., Shim, H., Cho, A., Kim, H., Hwang, S., Shim, J. E. and Lee, I. (2015) FlyNet: a versatile network prioritization server for the Drosophila community. Nucleic Acids Res., 43, W91-W97.
8. Pruitt, K. D., Harrow, J., Harte, R. A., Wallin, C., Diekhans, M., Maglott, D. R., Searle, S., Farrell, C. M., Loveland, J. E., Ruef, B. J. et al. (2009) The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes (vol 19, pg 1316, 2009). Genome Res., 19, 1506-1506.
9. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
10. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. and Yeates, T. O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. U. S. A., 96, 4285-4288.
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, 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.
13. Razick, S., Magklaras, G. and Donaldson, I. M. (2008) iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics, 9, 405.
14. Hwang, S., Rhee, S. Y., Marcotte, E. M. and Lee, I. (2011) Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat. Protoc., 6, 1429-1442.
15. Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
16. Schmitt, T., Ogris, C. and Sonnhammer, E. L. L. (2014) FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res., 42, D380-D388.
17. Guan, Y. F., Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J. and Troyanskaya, O. G. (2008) A Genomewide Functional Network for the Laboratory Mouse. PLoS Comput. Biol., 4, e1000165.
18. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
19. Smith, C. L. and Eppig, J. T. (2012) The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm. Genome, 23, 653-668.
20. Ruepp, A., Waegele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C. and Mewes, H. W. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res., 38, D497-D501.
21. Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R. et al. (2014) The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
22. Amberger, J. S., Bocchini, C. A., Schiettecatte, F., Scott, A. F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM (R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
23. Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 42, D1001-D1006.
24. 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.
25. Shim, J. E. and Lee, I. (2015) Network-assisted approaches for human disease research. Animal Cells Syst., 19, 231-235.
26. Welsby, I., Hutin, D., Gueydan, C., Kruys, V., Rongvaux, A. and Leo, O. (2014) PARP12, an Interferon-stimulated Gene Involved in the Control of Protein Translation and Inflammation. J. Biol. Chem., 289, 26642-26657.
27. Kohler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C. M., Brown, D. L., Brudno, M., Campbell, J. et al. (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res., 42, D966-D974.
28. Han, C., Choi, E., Park, I., Lee, B., Jin, S., Kim, D. H., Nishimura, H. and Cho, C. (2009) Comprehensive analysis of reproductive ADAMs: relationship of ADAM4 and ADAM6 with an ADAM complex required for fertilization in mice. Biol. Reprod., 80, 1001-1008.
29. Puthussery, T., Gayet-Primo, J. and Taylor, W. R. (2010) Localization of the calcium-binding protein secretagogin in cone bipolar cells of the mammalian retina. J. Comp. Neurol., 518, 513-525.
30. Turczynska, K. M., Sward, K., Hien, T. T., Wohlfahrt, J., Mattisson, I. Y., Ekman, M., Nilsson, J., Sjogren, J., Murugesan, V., Hultgardh-Nilsson, A. et al. (2015) Regulation of smooth muscle dystrophin and synaptopodin 2 expression by actin polymerization and vascular injury. Arterioscl. Throm. Vas., 35, 1489-1497.
31. Darnell, D. K., Kaur, S., Stanislaw, S., Davey, S., Konieczka, J. H., Yatskievych, T. A. and Antin, P. B. (2007) GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenet. Genome Res., 117, 30-35.