SoyFN: a knowledge database of soybean functional networks

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

doi:10.1093/database/bau019

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

Highlights

Soybean (Glycine max), an important domesticated species originating in China, constitutes a major source of edible oils and high-quality plant proteins worldwide
Many useful tools, including ID mapping, Motif scan, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Genome Browser are available for users to get more related information of the genes or miRNAs from the publicly accessed third-party databases
This section, as use cases, we describe two of the main implementations of SoyFN to show a miniature that SoyFN provides users with the integrative information of soybean genes and miRNAs, which will facilitate the researches for members of research communities both in soybean experimental science and bioinformatics

Summary

Introduction

Soybean (Glycine max), an important domesticated species originating in China, constitutes a major source of edible oils and high-quality plant proteins worldwide. SoyFN provides interfaces to freely retrieve, visualize, analyze and download the functional network of soybean genes and miRNAs. The SoyFN Web site can be used to access the integrative information about genome context provided by genome browser, participated pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology annotations (GOA) by UniProtKB and EnsemblPlants, etc., as well as to convert gene ID between different identifiers and to compute gene (or GO term) functional (or semantic) similarity by using our previously proposed method [19].

Results

Conclusion