Soybean Functional Network

        A database of Soybean Functional Gene Network (SoyFGN) and miRNA Functional Network (SoymiRFN)


                         Functional Gene Network (FGN) | miRNA Network (miRFN)
                                          miRNA-Target datasets | 3'-UTR | Gene Annotations| KEGG Pathway
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Scientific classification
Kingdom: Plantae
(unranked): Angiosperms
(unranked): Eudicots
(unranked): Rosids
Order: Fabales
Family: Fabaceae
Subfamily: Faboideae
Genus: Glycine
Species: G. max
Binomial name
Glycine max
(L.) Merr.
Synonyms[1]
  • Dolichos soja L.
  • Glycine angustifolia Miq.
  • Glycine gracilis Skvortsov
  • Glycine hispida (Moench) Maxim.
  • Glycine soja sensu auct.
  • Phaseolus max L.
  • Soja angustifolia Miq.
  • Soja hispida Moench
  • Soja japonica Savi
  • Soja max (L.) Piper
  • Soja soja H.Karst.
  • Soja viridis Savi

SoyFN

SoyFN: Soybean(Glycine max) Functional Network is a comprehensive web tool about soybean functional gene network (SoyFGN) and microRNA functional network (SoymiRFN). It contain all 37827 genes of the release of UniprotKB version 111 and all 555 mature miRNAs of the latest release of miRBase(Release 19: August 2012) . You can compute any pair of soybean genes or miRNAs and get genes' 3'-UTRs. By using Cytoscape Web, the user can easily view his/her interesting genes or miRNAs in a network. Also, KEGG pathway, motif and genome browser are incorporated to analysis other types of function of miRNA and target genes of Soybean. [More... ]

All genome datasets are of the Williams 82(Glam 1.1).

 

Glycine max

The soybean (US) or soya bean (UK) (Glycine max) is a species of legume native to East Asia, widely grown for its edible bean which has numerous uses. The plant is classed as an oilseed rather than a pulse by the UN Food and Agricultural Organization (FAO).

Fat-free (defatted) soybean meal is a significant and cheap source of protein for animal feeds and many prepackaged meals;soy vegetable oil is another product of processing the soybean crop. For example, soybean products such as textured vegetable protein (TVP) are ingredients in many meat and dairy analogues. Soybeans produce significantly more protein per acre than most other uses of land.

Traditional nonfermented food uses of soybeans include soy milk, and from the latter tofu and tofu skin. Fermented foods include soy sauce, fermented bean paste, natto, and tempeh, among others. The oil is used in many industrial applications. The main producers of soy are the United States (35%), Brazil (27%), Argentina (19%), China (6%) and India (4%).Today, the United States is also the world's largest consumer of soybeans, with an average annual consumption of 45,313 TMT. The beans contain significant amounts of phytic acid, alpha-linolenic acid, and isoflavones.     [More...]

Functional Modules


GFSAT The 'Gene Analysis Tool —GFSAT' is a web tool that can be used to Analysis the functional similarity of genes in the forms of "two genes", "two groups genes ", and "pairwise genes group" based on GO Annotation(GOA) and GO semantic similarity measurements. The semantic similarity measurements utilized by GFSAT 1.1 are SSDD, G-SESAME and simUI now. Soon, more and more algorithms will be integrated into.

SoyFGN SoyFGN: Soybean Functional Gene Network, is a network of soybean genes, constructed based on the functional similarity between gene pairs. The Functional similarity of pairwise genes were measured by GFSAT based on their GO Annotations (GOA).

miRFun miRFun is a method to compute the functional similaritiy of Soybean (Glycine max.) miRNAs by taking fully into account both the functional similarity between their targets and the regulatory strengths they exert on their targets.

miRFun firstly measures the regulatory strength based on site accessibility and the functional similarity between the target genes of two miRNAs based on a gene functional network (GFN). And further infer the functional similarity for these two miRNAs by integrating these two critical factors.

SoyModule allows users to retrieve, display, analysis, and download the bilayer functional modules of soybean miRNA-gene bilayer network in different hierarchical levels, identified by the proposed Psuedo-3D clustering algorithm.

SoymiRFN SoymiRFN: Soybean Functional miRNA Network, was constructed firstly by measuring the functional similarity of pairwise miRNAs taking fully account into both the regulatory strength based on site accessibility and the functional similarity between the target genes of two miRNAs based on their target gene functional networks (SoyGFNs). And secondly by setting a threshold to select the significant functional associations based on "Clustering coefficient".

Main Tools

Genome Browser A graphical interface for display of information  for genomic data. Genome browsers enable users to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Users can search and display the genome by using genome coordinate, gene name, valid ID of genes and miRNAs. Genome Browser provide not only the service of Soybean genome, but also that of Arabidopsis and Rice.

KEGG Pathway A tool can be used to retrieve the genes involved in specific KEGG pathways, and display them in a graphic view. Users can search by using the genes UniprotKB AC/IDs or Ensembl Genome IDs. Now only the genes of Soybean are supported.

Soybean eFP Create 'electronic fluorescent pictographic (eFP)' representations of your gene of interest's expression patterns based on two soybean data sets based on data from Libault et al.'s 2010 Plant Physiology and Plant Journalpapers.
GO Anotation A too to search the Gene Ontology Annotations (GOA) of a list of input genes. Two datasets are provided. They are GOA from UniprotKB and GOA from EnsemblPlants BioMart. Now only the genes of Soybean are supported. Motif Scan A tool can be used to search the motifs of the Soybean genes users input and analysis them.

  

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