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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Statistics

 
Statistics

Statistics of SoyFGN 1.0

      1. Information of Soybean Genes

         1. Sequence

           2. Genome coordinates

     2. Information of binding miRNAs

         1. Predicted binding miRNAs

           2. mRNA 3'-UTRs

     3. Pairwise functional similarity

         1. Heamap

           2. FS download (.txt)

    4. SoyFGN:Soybean functional gene network

         1. Global properties

           2. Degree distribution

           3. SoyFGN-INT in Genome

    5. Visit Statistic


 
UniprotKB: V111; EnsemblPlants: V1.0, JGI-Glyma-1.1; Gene Ontology: V1.1.3499
 
 

Section

Description

Number of genes

Genes: 37827

BP

Annotated by Biological Process

27594

MF

Annotated by Molecular Function

33189

CC

Annotated by Cellular Component

14150

GOA:165040

BP

Annotations of Biological Process

47452

MF

Annotations of Molecular Function

92374

CC

Annotations of Cellular Component

25214
GO:38137

BP

Biological Process

23928

MF

Molecular Function

9467

CC

Cellular Component

3050

 Obsolete

Obsoleted terms

1692

   
 

Download Coordinates
   



 
Genome Coordinates (Phytozome5.0)
Download Coordinates
   
   
   
   
     
Information of miRNA targets
 
The number of predicted target genes by three methods Download Targets
   


       
  Target 3'-UTR sequence (49942 in totall)
Download 3'-UTR
     
     
     
Information of pairwise genes functional similarity
     
  Heatmap of Functional Similarity
Download full size
   
     
     
     
     
  Functional Similairity batch download
Download full size
   
     
     
     
Soybean Functional Gene Network (SoyFGN)
     
  Global properties
   

Property

BP

MF

CC

Integration

Number of Nodes

25835

28833

14136

33087

Number of Edges

7366700

8552866

6144656

9187249

Cluster Coefficient

0.8521

0.9594

0.9107

0.7522

Connected components

137

119

76

38

Diameter

11

9

11

10

Radius

1

1

1

1

Centralisation

0.04196

0.07967

0.09372

0.1325

Shortest paths

9337684

1982914

1739716

51359370

Characteristic path length

3.366

2.0965

3.90382

3.7753

Avg. number of neighbors

139.7488

166.0099

128.96774

132.9974

Density

0.0221

0.0206

0.0615

0.0161

Heterogeneity

0.8835

0.9205

0.8464

1.0899

     
     
  Degree Distribution
   


Degree distributions and thier fitted models of four miRFNs


Joint degree distributions of four miRFNs


K-nearest neighbours and Pearson Correlation of degree (PCD) distributuon

     
     
  SoyFGN in Genome(of Integration, SoyFGN-INT)
   
     
 

Statistics of SoymiRFN

      1. Information of Soybean miRNAs

         1. Sequence

           2. Genome coordinates

     2. Information of miRNA targets

         1. Predicted targets

           2. Target 3'-UTRs

     3. Pairwise functional similarity

         1. Heamap

           2. FS download (.txt)

    4. miRFN: miRNA functional network

         1. Global properties

           2. Degree distribution

           3. SoymiRFN in Genome

    5. Visit Statistic


 

miRBase Release 19: Aug. 2012
Valid for Release 20: June 2013
3 Changes: gma-MIR167h(MI0017914) changed sequence; gma-MIR1513d(MI0017914)and gma-miR1513d(MIMAT0023180) were deleted

 

Section

Description

Number of hits

miRNA name

match the accession or ID of a hairpin precursor entry

506

Previous ID

match the previous ID of a hairpin precursor entry

29

Mature name

match the accession or ID of a mature miRNA sequence

555

Previous Mature ID

match the previous mature ID of a mature entry

61

Dead entry

match the accession or ID of a dead entry

0

Dead entry previous ID

match the accession or ID of a dead entry

0

Gene symbol

find miRNA entries based on gene symbols

0

Description

search miRNA entry description

0

Comments

search miRNA entry comments

0

PubMed ID

find miRNA entries based on literature reference PubMed ID

0

Literature reference

search title and authors of associated literature references

0

   
 

Download Coordinates
   



 
Genome Coordinates (Phytozome5.0)
Download Coordinates
   
   
   
   
     
Information of miRNA targets
 
The number of predicted target genes by three methods Download Targets
   


       
  Target 3'-UTR sequence (49942 in totall)
Download 3'-UTR
     
     
     
Information of pairwise miRNAs functional similarity
     
  Heatmap of Functional Similarity
Download full size
   
     
     
     
     
  Functional Similairity batch download
Download full size
   
     
     
     
miRNA Functional Network (miRFN)
     
  Global properties
   

Property

BP

MF

CC

Integration

Number of Nodes

462

454

512

472

Number of Edges

7858

8271

16813

7038

Cluster Coefficient

0.782

0.779

0.832

0.762

Connected components

13

15

5

11

Diameter

6

5

6

7

Radius

1

1

1

1

Centralization

0.503

0.467

0.511

0.487

Shortest paths

185394

162316

253520

193276

Characteristic path length

2.372

2.287

2.104

2.573

Avg. number of neighbors

34.017

36.436

65.676

29.822

Density

0.074

0.080

0.129

0.063

Heterogeneity

1.281

1.292

1.135

1.323

     
     
  Degree Distribution
   


Degree distributions and thier fitted models of four miRFNs


Joint degree distributions of four miRFNs


K-nearest neighbours and Pearson Correlation of degree (PCD) distributuon

     
     
  SoymiRFN in Genome(of Integration)
   
     
 

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