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Database (Oxford). 2014 Mar 10;2014:bau019. doi: 10.1093/database/bau019. Print 2014.

SoyFN: a knowledge database of soybean functional networks.

Author information

1
School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China and School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China.

Abstract

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

PMID:
24618044
PMCID:
PMC3949006
DOI:
10.1093/database/bau019
[Indexed for MEDLINE]
Free PMC Article

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