GCA_001420915_01068 protein (Agarivorans gilvus)

Nodes:

Network nodes represent proteins

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

Node Color

colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
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:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

GCA_001420915_01068

Unannotated protein. (415 aa)

Predicted Functional Partners:

GCA_001420915_01069

0.998

GCA_001420915_01071

0.996

GCA_001420915_01070

0.987

GCA_001420915_01072

0.962

GCA_001420915_01074

0.960

GCA_001420915_01075

0.938

GCA_001420915_01076

0.937

GCA_001420915_01073

0.912

GCA_001420915_01370

0.809

GCA_001420915_04319

0.622

Your Current Organism:

Agarivorans gilvus

NCBI taxonomy Id: 680279
Other names: A. gilvus, Agarivorans gilvus Du et al. 2011, Agarivorans sp. WH0801, CGMCC 1.10131, NRRL B-59247, strain WH0801

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structured XML interaction data, according to the 'PSI-MI' data standard

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... functional annotations:

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Browse interactions in tabular form:

node1	node2	node1 annotation	node2 annotation	score
GCA_001420915_01068	GCA_001420915_01069	Unannotated protein.	Unannotated protein.	0.998
GCA_001420915_01068	GCA_001420915_01070	Unannotated protein.	Unannotated protein.	0.987
GCA_001420915_01068	GCA_001420915_01071	Unannotated protein.	Unannotated protein.	0.996
GCA_001420915_01068	GCA_001420915_01072	Unannotated protein.	Unannotated protein.	0.962
GCA_001420915_01068	GCA_001420915_01073	Unannotated protein.	Unannotated protein.	0.912
GCA_001420915_01068	GCA_001420915_01074	Unannotated protein.	Unannotated protein.	0.960
GCA_001420915_01068	GCA_001420915_01075	Unannotated protein.	Unannotated protein.	0.938
GCA_001420915_01068	GCA_001420915_01076	Unannotated protein.	Unannotated protein.	0.937
GCA_001420915_01068	GCA_001420915_01370	Unannotated protein.	Unannotated protein.	0.809
GCA_001420915_01068	GCA_001420915_04319	Unannotated protein.	Unannotated protein.	0.622
GCA_001420915_01069	GCA_001420915_01068	Unannotated protein.	Unannotated protein.	0.998
GCA_001420915_01069	GCA_001420915_01070	Unannotated protein.	Unannotated protein.	0.991
GCA_001420915_01069	GCA_001420915_01071	Unannotated protein.	Unannotated protein.	0.995
GCA_001420915_01069	GCA_001420915_01072	Unannotated protein.	Unannotated protein.	0.967
GCA_001420915_01069	GCA_001420915_01073	Unannotated protein.	Unannotated protein.	0.905
GCA_001420915_01069	GCA_001420915_01074	Unannotated protein.	Unannotated protein.	0.966
GCA_001420915_01069	GCA_001420915_01075	Unannotated protein.	Unannotated protein.	0.947
GCA_001420915_01069	GCA_001420915_01076	Unannotated protein.	Unannotated protein.	0.948
GCA_001420915_01070	GCA_001420915_01068	Unannotated protein.	Unannotated protein.	0.987
GCA_001420915_01070	GCA_001420915_01069	Unannotated protein.	Unannotated protein.	0.991

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

25

average node degree:

4.55

avg. local clustering coefficient:

0.676

expected number of edges:

16

PPI enrichment p-value:

0.0223

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

6 of 179

1.86

2.89

1.81e-07

GO:0006351

Transcription, DNA-templated

7 of 313

1.69

2.59

1.81e-07

GO:0006367

Transcription initiation from RNA polymerase II promoter

3 of 33

2.3

1.83

0.00034

GO:0045948

Positive regulation of translational initiation

2 of 19

2.36

1.0

0.0148

GO:0030150

Protein import into mitochondrial matrix

2 of 23

2.28

0.92

0.0199

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003899

DNA-directed 5-3 RNA polymerase activity

4 of 21

2.62

3.24

8.12e-07

GO:0031369

Translation initiation factor binding

2 of 17

2.41

1.0

0.0146

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005665

RNA polymerase II, core complex

5 of 14

2.89

5.66

2.56e-11

GO:0055029

Nuclear DNA-directed RNA polymerase complex

7 of 97

2.2

5.0

9.66e-12

GO:0016591

RNA polymerase II, holoenzyme

6 of 71

2.27

4.73

1.04e-10

GO:0005744

TIM23 mitochondrial import inner membrane translocase complex

2 of 9

2.69

1.65

0.00095

GO:0005654

Nucleoplasm

7 of 2180

0.85

0.7

0.0010

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:9495

RNA polymerase II, core complex

5 of 8

3.13

5.64

4.38e-11

CL:9468

RNA Polymerase II Pre-transcription Events, and RNA Polymerase III Transcription Initiation From Type 1 Promoter

7 of 181

1.93

3.78

6.36e-10

CL:9476

RNA Polymerase II Pre-transcription Events, and Transcription elongation factor complex

6 of 126

2.02

3.59

8.63e-09

CL:32588

Mitochondrial protein import, and Protein insertion into mitochondrial inner membrane

3 of 38

2.24

1.82

0.00034

CL:32638

TIM23 mitochondrial import inner membrane translocase complex

2 of 5

2.94

1.54

0.0016

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03020

RNA polymerase

6 of 54

2.38

5.25

1.69e-11

map04623

Cytosolic DNA-sensing pathway

2 of 68

1.81

0.71

0.0443

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-6803529

FGFR2 alternative splicing

6 of 27

2.69

5.95

3.21e-12

MAP-77075

RNA Pol II CTD phosphorylation and interaction with CE

6 of 32

2.61

5.83

4.00e-12

MAP-72086

mRNA Capping

6 of 33

2.6

5.81

4.00e-12

MAP-113418

Formation of the Early Elongation Complex

6 of 36

2.56

5.77

4.00e-12

MAP-76042

RNA Polymerase II Transcription Initiation And Promoter Clearance

6 of 52

2.4

5.21

2.34e-11

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

7 of 94

2.21

5.03

9.54e-12

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

6 of 81

2.21

4.39

4.47e-10

GOCC:0005665

RNA polymerase II, core complex

3 of 8

2.91

2.97

3.65e-06

GOCC:0016591

RNA polymerase II, holoenzyme

4 of 59

2.17

2.71

3.65e-06

GOCC:0005744

TIM23 mitochondrial import inner membrane translocase complex

2 of 9

2.69

1.55

0.0015

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

6 of 30

2.64

6.1

1.23e-12

KW-0804

Transcription

7 of 517

1.47

2.18

1.26e-07

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00662

RNA polymerases D

2 of 2

3.34

1.69

0.00092

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