GCA_002087335_03062 protein (Pseudophaeobacter leonis)

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_002087335_03062

Unannotated protein. (97 aa)

Predicted Functional Partners:

GCA_002087335_03060

0.999

GCA_002087335_03063

0.995

GCA_002087335_03061

0.994

GCA_002087335_01061

0.955

GCA_002087335_02095

0.946

GCA_002087335_03227

0.937

GCA_002087335_00013

0.926

GCA_002087335_00014

0.916

GCA_002087335_04992

0.912

GCA_002087335_04993

0.912

Your Current Organism:

Pseudophaeobacter leonis

NCBI taxonomy Id: 1144477
Other names: CIP 110369, DSM 25627, P. leonis, Phaeobacter leonis, Phaeobacter leonis Gaboyer et al. 2013, Phaeobacter sp. 306, Pseudophaeobacter leonis (Gaboyer et al. 2013) Breider et al. 2014, UBOCC 3187, strain 306

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

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

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 annotation	node2 annotation	score
GCA_002087335_00013	GCA_002087335_00014	Unannotated protein.	Unannotated protein.	0.994
GCA_002087335_00013	GCA_002087335_01061	Unannotated protein.	Unannotated protein.	0.998
GCA_002087335_00013	GCA_002087335_02095	Unannotated protein.	Unannotated protein.	0.989
GCA_002087335_00013	GCA_002087335_03061	Unannotated protein.	Unannotated protein.	0.920
GCA_002087335_00013	GCA_002087335_03062	Unannotated protein.	Unannotated protein.	0.926
GCA_002087335_00013	GCA_002087335_03227	Unannotated protein.	Unannotated protein.	0.959
GCA_002087335_00013	GCA_002087335_04992	Unannotated protein.	Unannotated protein.	0.841
GCA_002087335_00013	GCA_002087335_04993	Unannotated protein.	Unannotated protein.	0.843
GCA_002087335_00014	GCA_002087335_00013	Unannotated protein.	Unannotated protein.	0.994
GCA_002087335_00014	GCA_002087335_01061	Unannotated protein.	Unannotated protein.	0.992
GCA_002087335_00014	GCA_002087335_02095	Unannotated protein.	Unannotated protein.	0.984
GCA_002087335_00014	GCA_002087335_03061	Unannotated protein.	Unannotated protein.	0.904
GCA_002087335_00014	GCA_002087335_03062	Unannotated protein.	Unannotated protein.	0.916
GCA_002087335_00014	GCA_002087335_03227	Unannotated protein.	Unannotated protein.	0.948
GCA_002087335_00014	GCA_002087335_04992	Unannotated protein.	Unannotated protein.	0.838
GCA_002087335_00014	GCA_002087335_04993	Unannotated protein.	Unannotated protein.	0.839
GCA_002087335_01061	GCA_002087335_00013	Unannotated protein.	Unannotated protein.	0.998
GCA_002087335_01061	GCA_002087335_00014	Unannotated protein.	Unannotated protein.	0.992
GCA_002087335_01061	GCA_002087335_02095	Unannotated protein.	Unannotated protein.	0.997
GCA_002087335_01061	GCA_002087335_03061	Unannotated protein.	Unannotated protein.	0.952

page 1 of 5

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

23

PPI enrichment p-value:

6.55e-09

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:0006351

Transcription, DNA-templated

9 of 259

1.88

4.47

5.53e-13

GO:0006366

Transcription by RNA polymerase II

5 of 82

2.12

3.28

1.37e-07

GO:0031990

mRNA export from nucleus in response to heat stress

2 of 2

3.34

2.04

0.00021

GO:0006367

Transcription initiation from RNA polymerase II promoter

3 of 37

2.25

2.01

0.00014

GO:0034402

Recruitment of 3-end processing factors to RNA polymerase II holoenzyme complex

2 of 3

3.16

1.93

0.00033

(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

7 of 37

2.62

6.82

2.93e-14

GO:0031369

Translation initiation factor binding

2 of 16

2.44

1.15

0.0077

GO:0003677

DNA binding

6 of 2294

0.76

0.42

0.0448

GO:1901363

Heterocyclic compound binding

10 of 7560

0.46

0.33

0.0180

GO:0097159

Organic cyclic compound binding

10 of 7587

0.46

0.33

0.0180

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005665

RNA polymerase II, core complex

8 of 18

2.99

10.15

4.24e-20

GO:0055029

Nuclear DNA-directed RNA polymerase complex

10 of 106

2.31

8.26

4.24e-20

GO:0005736

RNA polymerase I complex

4 of 14

2.79

4.44

5.02e-09

GO:0005666

RNA polymerase III complex

4 of 23

2.58

3.98

2.46e-08

GO:0005730

Nucleolus

5 of 329

1.52

1.88

9.04e-06

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:9014

RNA polymerase II, core complex, and Transcription elongation factor, TFIIS

9 of 20

2.99

11.17

3.60e-22

CL:9021

RNA polymerase II, core complex

7 of 10

3.18

9.4

3.36e-18

CL:8998

RNA Polymerase II Pre-transcription Events, and RNA Polymerase III Transcription

11 of 151

2.2

8.08

2.23e-21

CL:9026

RNA polymerase II, core complex

5 of 5

3.34

6.68

6.42e-13

CL:9230

RNA Polymerase III Transcription, and RNA Polymerase I Transcription Initiation

2 of 34

2.11

0.75

0.0406

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

nnu03020

RNA polymerase

10 of 36

2.78

12.06

3.41e-25

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-9018519

Estrogen-dependent gene expression

9 of 49

2.6

9.37

3.39e-20

MAP-77075

RNA Pol II CTD phosphorylation and interaction with CE

9 of 50

2.59

9.35

3.39e-20

MAP-72086

mRNA Capping

9 of 52

2.58

9.3

3.39e-20

MAP-6807505

RNA polymerase II transcribes snRNA genes

10 of 78

2.45

9.27

2.40e-21

MAP-113418

Formation of the Early Elongation Complex

9 of 55

2.55

9.21

3.51e-20

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

10 of 92

2.37

8.66

1.79e-20

GOCC:0005665

RNA polymerase II, core complex

4 of 7

3.1

4.81

1.50e-09

GOCC:0005736

RNA polymerase I complex

4 of 11

2.9

4.46

5.43e-09

GOCC:0000419

RNA polymerase V complex

3 of 10

2.82

3.11

1.82e-06

GOCC:0031981

Nuclear lumen

8 of 838

1.32

1.89

5.15e-08

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

10 of 47

2.67

11.08

8.31e-24

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF03871

RNA polymerase Rpb5, N-terminal domain

2 of 2

3.34

1.46

0.0024

PF01191

RNA polymerase Rpb5, C-terminal domain

2 of 2

3.34

1.46

0.0024

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR045222

DNA-directed RNA polymerase II subunit Rpb4-like

3 of 3

3.34

2.79

9.05e-06

IPR038324

Rpb4/RPC9 superfamily

3 of 4

3.21

2.79

9.05e-06

IPR006590

RNA polymerase Rpb4/RPC9, core

3 of 4

3.21

2.79

9.05e-06

IPR005574

RNA polymerase subunit Rpb4/RPC9

3 of 4

3.21

2.79

9.05e-06

IPR010997

HRDC-like superfamily

3 of 8

2.91

2.64

1.49e-05

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00657

DNA-directed RNA-polymerase II subunit

3 of 4

3.21

3.24

1.34e-06

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (30%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About