tbc1d2b protein (Oryzias latipes) - STRING interaction network

Nodes:

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second shell of interactors

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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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Gene Fusion

Cooccurrence

Coexpression

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[Homology]

Score

tbc1d2b

TBC1 domain family, member 2B. (970 aa)

Predicted Functional Partners:

rab7a

0.667

LOC101157689

0.667

Wdr90

0.562

ENSORLP00000042816

0.562

nrde2

0.497

mrpl11

0.483

cfap126

0.478

ENSORLP00000041141

0.473

pacrg

0.468

armc5

0.466

Your Current Organism:

Oryzias latipes

NCBI taxonomy Id: 8090
Other names: Japanese medaka, Japanese rice fish, O. latipes, Poecilia latipes, medaka

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
ENSORLP00000041141	ENSORLP00000042816	ENSORLP00000041141	ENSORLP00000042816	Uncharacterized protein.	Uncharacterized protein.	0.830
ENSORLP00000041141	Wdr90	ENSORLP00000041141	ENSORLP00000039753	Uncharacterized protein.	WD_REPEATS_REGION domain-containing protein.	0.830
ENSORLP00000041141	cfap126	ENSORLP00000041141	ENSORLP00000041374	Uncharacterized protein.	Cilia and flagella associated protein 126.	0.882
ENSORLP00000041141	pacrg	ENSORLP00000041141	ENSORLP00000035115	Uncharacterized protein.	PARK2 co-regulated.	0.792
ENSORLP00000041141	tbc1d2b	ENSORLP00000041141	ENSORLP00000041335	Uncharacterized protein.	TBC1 domain family, member 2B.	0.473
ENSORLP00000042816	ENSORLP00000041141	ENSORLP00000042816	ENSORLP00000041141	Uncharacterized protein.	Uncharacterized protein.	0.830
ENSORLP00000042816	Wdr90	ENSORLP00000042816	ENSORLP00000039753	Uncharacterized protein.	WD_REPEATS_REGION domain-containing protein.	0.960
ENSORLP00000042816	cfap126	ENSORLP00000042816	ENSORLP00000041374	Uncharacterized protein.	Cilia and flagella associated protein 126.	0.830
ENSORLP00000042816	pacrg	ENSORLP00000042816	ENSORLP00000035115	Uncharacterized protein.	PARK2 co-regulated.	0.910
ENSORLP00000042816	tbc1d2b	ENSORLP00000042816	ENSORLP00000041335	Uncharacterized protein.	TBC1 domain family, member 2B.	0.562
LOC101157689	rab7a	ENSORLP00000027914	ENSORLP00000021124	RAB7a, member RAS oncogene family.	Uncharacterized protein.	0.900
LOC101157689	tbc1d2b	ENSORLP00000027914	ENSORLP00000041335	RAB7a, member RAS oncogene family.	TBC1 domain family, member 2B.	0.667
Wdr90	ENSORLP00000041141	ENSORLP00000039753	ENSORLP00000041141	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.830
Wdr90	ENSORLP00000042816	ENSORLP00000039753	ENSORLP00000042816	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.960
Wdr90	cfap126	ENSORLP00000039753	ENSORLP00000041374	WD_REPEATS_REGION domain-containing protein.	Cilia and flagella associated protein 126.	0.830
Wdr90	pacrg	ENSORLP00000039753	ENSORLP00000035115	WD_REPEATS_REGION domain-containing protein.	PARK2 co-regulated.	0.910
Wdr90	tbc1d2b	ENSORLP00000039753	ENSORLP00000041335	WD_REPEATS_REGION domain-containing protein.	TBC1 domain family, member 2B.	0.562
armc5	tbc1d2b	ENSORLP00000002620	ENSORLP00000041335	Armadillo repeat containing 5.	TBC1 domain family, member 2B.	0.466
cfap126	ENSORLP00000041141	ENSORLP00000041374	ENSORLP00000041141	Cilia and flagella associated protein 126.	Uncharacterized protein.	0.882
cfap126	ENSORLP00000042816	ENSORLP00000041374	ENSORLP00000042816	Cilia and flagella associated protein 126.	Uncharacterized protein.	0.830

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

39

average node degree:

7.09

avg. local clustering coefficient:

0.968

expected number of edges:

11

PPI enrichment p-value:

3.84e-11

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:0006525

Arginine metabolic process

11 of 34

2.23

8.23

2.82e-21

GO:0006526

Arginine biosynthetic process

9 of 17

2.45

8.04

4.90e-18

GO:0006591

Ornithine metabolic process

4 of 6

2.55

3.56

1.65e-07

GO:0042450

Arginine biosynthetic process via ornithine

2 of 2

2.72

1.57

0.0014

GO:0044205

De novo UMP biosynthetic process

2 of 7

2.18

1.12

0.0079

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0103045

Methione N-acyltransferase activity

2 of 2

2.72

0.93

0.0203

GO:0004088

Carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity

2 of 2

2.72

0.93

0.0203

GO:0004042

acetyl-CoA:L-glutamate N-acetyltransferase activity

2 of 2

2.72

0.93

0.0203

GO:0016774

Phosphotransferase activity, carboxyl group as acceptor

2 of 7

2.18

0.82

0.0303

GO:0016879

Ligase activity, forming carbon-nitrogen bonds

3 of 51

1.49

0.73

0.0303

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005737

Cytoplasm

11 of 1829

0.5

0.42

0.00052

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1505

Arginine biosynthesis, and Amino acid antiporter

9 of 15

2.5

8.22

4.37e-18

CL:1510

Arginine biosynthesis

6 of 6

2.72

6.12

1.70e-12

CL:1367

Cellular amino acid biosynthetic process, and Ribonucleoside monophosphate biosynthetic process

11 of 152

1.58

3.6

3.78e-15

CL:1525

Amino acid antiporter, and Arginine catabolic process to ornithine

2 of 5

2.33

1.03

0.0127

CL:1578

Pyrimidine biosynthesis, and Dihydroorotase, conserved site

2 of 6

2.25

0.99

0.0148

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

pfn00220

Arginine biosynthesis

9 of 36

2.12

6.25

3.12e-16

pfn00250

Alanine, aspartate and glutamate metabolism

4 of 39

1.74

1.95

3.78e-05

pfn01230

Biosynthesis of amino acids

7 of 179

1.32

1.75

6.17e-07

pfn01210

2-Oxocarboxylic acid metabolism

4 of 51

1.62

1.75

6.84e-05

pfn01110

Biosynthesis of secondary metabolites

8 of 614

0.84

0.78

6.84e-05

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005951

Carbamoyl-phosphate synthase complex

2 of 2

2.72

1.18

0.0073

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0055

Arginine biosynthesis

9 of 13

2.56

8.87

2.96e-19

KW-0963

Cytoplasm

8 of 311

1.13

1.38

8.14e-07

KW-0665

Pyrimidine biosynthesis

2 of 10

2.03

1.0

0.0124

KW-0436

Ligase

3 of 73

1.34

0.8

0.0152

KW-0808

Transferase

5 of 407

0.81

0.51

0.0216

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00696

Amino acid kinase family

3 of 6

2.42

1.85

0.00035

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR036393

Acetylglutamate kinase-like superfamily

3 of 6

2.42

1.71

0.00065

IPR001048

Aspartate/glutamate/uridylate kinase

3 of 6

2.42

1.71

0.00065

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