Vbra_21119 protein (Vitrella brassicaformis)

Nodes:

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splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

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query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

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proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

Edges represent protein-protein associations

associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.

Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

Others

textmining

co-expression

protein homology

Your Input:

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[Homology]

Score

Vbra_21119

Uncharacterized protein. (394 aa)

Predicted Functional Partners:

Vbra_22761

0.841

Vbra_11708

0.818

Vbra_12156

0.817

Vbra_13269

0.817

Vbra_11734

0.753

Vbra_5720

0.731

Vbra_9208

0.696

Vbra_9046

0.692

Vbra_5258

0.683

Vbra_9663

0.683

Your Current Organism:

Vitrella brassicaformis

NCBI taxonomy Id: 1169540
Other names: V. brassicaformis CCMP3155, Vitrella brassicaformis CCMP3155

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
Vbra_11708	Vbra_21119	A0A0G4EHB2	A0A0G4EX67	Uncharacterized protein.	Uncharacterized protein.	0.818
Vbra_11708	Vbra_22761	A0A0G4EHB2	A0A0G4GI06	Uncharacterized protein.	CDC73_C domain-containing protein.	0.997
Vbra_11708	Vbra_5720	A0A0G4EHB2	A0A0G4F3A8	Uncharacterized protein.	CPSF_A domain-containing protein.	0.665
Vbra_11734	Vbra_21119	A0A0G4EH15	A0A0G4EX67	Uncharacterized protein.	Uncharacterized protein.	0.753
Vbra_12156	Vbra_21119	A0A0G4EJS4	A0A0G4EX67	Uncharacterized protein.	Uncharacterized protein.	0.817
Vbra_12156	Vbra_9208	A0A0G4EJS4	A0A0G4FHX1	Uncharacterized protein.	Tr-type G domain-containing protein.	0.829
Vbra_13269	Vbra_21119	A0A0G4ETU6	A0A0G4EX67	Uncharacterized protein.	Uncharacterized protein.	0.817
Vbra_13269	Vbra_9208	A0A0G4ETU6	A0A0G4FHX1	Uncharacterized protein.	Tr-type G domain-containing protein.	0.829
Vbra_21119	Vbra_11708	A0A0G4EX67	A0A0G4EHB2	Uncharacterized protein.	Uncharacterized protein.	0.818
Vbra_21119	Vbra_11734	A0A0G4EX67	A0A0G4EH15	Uncharacterized protein.	Uncharacterized protein.	0.753
Vbra_21119	Vbra_12156	A0A0G4EX67	A0A0G4EJS4	Uncharacterized protein.	Uncharacterized protein.	0.817
Vbra_21119	Vbra_13269	A0A0G4EX67	A0A0G4ETU6	Uncharacterized protein.	Uncharacterized protein.	0.817
Vbra_21119	Vbra_22761	A0A0G4EX67	A0A0G4GI06	Uncharacterized protein.	CDC73_C domain-containing protein.	0.841
Vbra_21119	Vbra_5258	A0A0G4EX67	A0A0G4ENA0	Uncharacterized protein.	Cytochrome c domain-containing protein; Belongs to the cytochrome c family.	0.683
Vbra_21119	Vbra_5720	A0A0G4EX67	A0A0G4F3A8	Uncharacterized protein.	CPSF_A domain-containing protein.	0.731
Vbra_21119	Vbra_9046	A0A0G4EX67	A0A0G4FD52	Uncharacterized protein.	Uncharacterized protein.	0.692
Vbra_21119	Vbra_9208	A0A0G4EX67	A0A0G4FHX1	Uncharacterized protein.	Tr-type G domain-containing protein.	0.696
Vbra_21119	Vbra_9663	A0A0G4EX67	A0A0G4G513	Uncharacterized protein.	Cytochrome c domain-containing protein; Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.	0.683
Vbra_22761	Vbra_11708	A0A0G4GI06	A0A0G4EHB2	CDC73_C domain-containing protein.	Uncharacterized protein.	0.997
Vbra_22761	Vbra_21119	A0A0G4GI06	A0A0G4EX67	CDC73_C domain-containing protein.	Uncharacterized protein.	0.841

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

50

average node degree:

9.09

avg. local clustering coefficient:

0.949

expected number of edges:

23

PPI enrichment p-value:

5.72e-07

your network has significantly more interactions
than expected (what does that mean?)

Functional enrichments in your networkNote: some enrichments may be expected here (why?)
disable highlight explain columns

Biological Process (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0006366

Transcription by RNA polymerase II

9 of 91

1.9

4.59

3.78e-13

GO:0001172

Transcription, RNA-templated

3 of 6

2.61

2.5

2.20e-05

GO:0006383

Transcription by RNA polymerase III

3 of 21

2.06

1.71

0.00045

GO:0006360

Transcription by RNA polymerase I

3 of 22

2.04

1.68

0.00049

GO:0045948

Positive regulation of translational initiation

2 of 3

2.73

1.51

0.0018

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003899

DNA-directed 5-3 RNA polymerase activity

5 of 25

2.21

3.28

2.16e-07

GO:0031369

Translation initiation factor binding

2 of 10

2.21

1.04

0.0118

GO:0003677

DNA binding

7 of 602

0.97

0.86

0.00045

GO:0003676

Nucleic acid binding

9 of 1218

0.78

0.68

0.00023

GO:1901363

Heterocyclic compound binding

10 of 2361

0.53

0.41

0.0029

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005665

RNA polymerase II, core complex

9 of 13

2.75

9.83

2.35e-20

GO:0005654

Nucleoplasm

11 of 218

1.61

3.81

7.10e-16

GO:0005736

RNA polymerase I complex

3 of 11

2.34

2.42

2.34e-05

GO:0005666

RNA polymerase III complex

3 of 15

2.21

4.96e-05

GO:0032044

DSIF complex

2 of 2

2.91

1.93

0.00031

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1772

RNA polymerase II, core complex

9 of 11

2.82

10.07

1.54e-20

CL:1776

RNA polymerase II, core complex

6 of 6

2.91

6.89

9.94e-14

CL:1686

DNA-directed RNA polymerase complex, and Regulation of DNA-templated transcription, elongation

11 of 126

1.85

5.37

3.79e-18

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03020

RNA polymerase

9 of 45

2.21

6.85

4.61e-17

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-113418

Formation of the Early Elongation Complex

11 of 32

2.44

10.14

7.67e-24

MAP-6796648

TP53 Regulates Transcription of DNA Repair Genes

11 of 40

2.35

9.43

3.17e-23

MAP-75955

RNA Polymerase II Transcription Elongation

11 of 43

2.32

9.22

4.25e-23

MAP-77075

RNA Pol II CTD phosphorylation and interaction with CE

10 of 30

2.43

9.19

2.51e-21

MAP-72086

mRNA Capping

10 of 32

2.4

9.05

2.90e-21

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

8 of 85

1.88

4.11

1.61e-11

GOCC:0005665

RNA polymerase II, core complex

4 of 5

2.81

3.99

3.79e-08

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

5 of 58

1.84

2.6

1.08e-06

GOCC:0005736

RNA polymerase I complex

2 of 5

2.51

1.43

0.0023

GOCC:0005654

Nucleoplasm

5 of 236

1.23

1.11

0.00060

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0804

Transcription

4 of 109

1.47

1.18

0.0018

KW-0240

DNA-directed RNA polymerase

2 of 14

2.06

0.91

0.0192

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