SoyFN: A knowledge database of soybean functional networks

Database

Volumn 2014, Issue , 2014, Pages

  Xu, Yungang ^a   Guo, Maozu ^a   Liu, Xiaoyan ^a   Wang, Chunyu ^a   Liu, Yang ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; COMPUTER PROGRAM; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; KNOWLEDGE BASE; METABOLISM; SEARCH ENGINE; SOYBEAN; STATISTICS;

DATABASES, GENETIC; GENE REGULATORY NETWORKS; KNOWLEDGE BASES; MICRORNAS; SEARCH ENGINE; SOFTWARE; SOYBEANS; STATISTICS AS TOPIC;

EID: 84906546983     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau019     Document Type: Article

References (21)

1. Shultz, J.L., Kurunam, D., Shopinski, K. et al. (2006) The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res., 34, D758-D765.
2. Cheng, K.C. and Strömvik, M.V. (2008) SoyXpress: a database for exploring the soybean transcriptome. BMC Genomics, 9, 368.
3. Grant, D., Nelson, R.T., Cannon, S.B. et al. (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res., 38, D843-D846.
4. Wang, Z., Libault, M., Joshi, T. et al. (2010) SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol., 10, 14.
5. Joshi, T., Patil, K., Fitzpatrick, M.R. et al. (2012) Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics, 13, S15.
6. Lee, I., Li, Z. and Marcotte, E.M. (2007) An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One, 2, e988.
7. Lee, I., Lehner, B., Crombie, C. et al. (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. et al. (2010) Predicting genetic modifier loci using functional gene networks. Genome Res., 20, 1143-1153.
9. Lee, I., Ambaru, B., Thakkar, P. et al. (2010a) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol., 28, 149-156.
10. Hwang, S., Rhee, S.Y., Marcotte, E.M. et al. (2011) Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat. Protoc., 6, 1429-1442.
11. Lee, I., Seo, Y.-S., Coltrane, D. et al. (2011b) Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc. Natl Acad. Sci. USA, 108, 18548-18553.
12. Guan, Y., Myers, C.L., Lu, R. et al. (2008) A genomewide functional network for the laboratory mouse. PLoS Comput. Biol., 4, e1000165.
13. 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.
14. Peña-Castillo, L., Tasan, M., Myers, C.L. et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol., 9, S2.
15. Lee, I., Blom, U.M., Wang, P.I. et al. (2011a) Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res., 21, 1109-1121.
16. Kersey, P.J., Staines, D.M., Lawson, D. et al. (2012) Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res., 40, D91-D97.
17. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
18. Xu, Y., Guo, M., Liu, X. et al. (2014) Inferring the soybean (Glycine max) microRNA functional network based on target gene network. Bioinformatics, 30, 94-103.
19. Xu, Y., Guo, M., Shi, W. et al. (2013) A novel insight into Gene Ontology semantic similarity. Genomics, 101, 368-375.
20. Kertesz, M., Iovino, N., Unnerstall, U. et al. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
21. Lopes, C.T., Franz, M., Kazi, F. et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.