A0A0P0YBE6 protein (Oryza sativa Japonica) - STRING interaction network

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second shell of interactors

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a 3D structure is known or predicted

Edges:

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Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

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textmining

co-expression

protein homology

Your Input:

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Score

A0A0P0YBE6

Os12g0562700 protein. (994 aa)

Predicted Functional Partners:

A0A0P0V1T6

0.717

A0A0P0WF03

0.711

Q7XM41_ORYSJ

0.678

Q0D3X3_ORYSJ

0.677

Q0JES2_ORYSJ

0.677

mrp8

0.676

Q0JA19_ORYSJ

0.671

Q6Z9U8_ORYSJ

0.671

A0A0P0VHR5

0.663

A0A0N7KF42

0.658

Your Current Organism:

Oryza sativa Japonica

NCBI taxonomy Id: 39947
Other names: Japanese rice, Japonica rice, O. sativa Japonica Group, Oryza sativa (japonica cultivar-group), Oryza sativa Japonica Group, Oryza sativa subsp. japonica

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
A0A0N7KF42	A0A0P0V1T6	A0A0N7KF42	A0A0P0V1T6	Os02g0288400 protein.	Os01g0314700 protein.	0.717
A0A0N7KF42	A0A0P0WF03	A0A0N7KF42	A0A0P0WF03	Os02g0288400 protein.	Os04g0620066 protein.	0.450
A0A0N7KF42	A0A0P0YBE6	A0A0N7KF42	A0A0P0YBE6	Os02g0288400 protein.	Os12g0562700 protein.	0.658
A0A0N7KF42	Q0D3X3_ORYSJ	A0A0N7KF42	Q0D3X3	Os02g0288400 protein.	Ubiquitin carboxyl-terminal hydrolase; Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Belongs to the peptidase C19 family.	0.677
A0A0N7KF42	Q0JES2_ORYSJ	A0A0N7KF42	Q0JES2	Os02g0288400 protein.	Os04g0209200 protein.	0.431
A0A0N7KF42	Q7XM41_ORYSJ	A0A0N7KF42	Q7XM41	Os02g0288400 protein.	cDNA clone:J013026A05, full insert sequence.	0.433
A0A0N7KF42	mrp8	A0A0N7KF42	Q8GU64	Os02g0288400 protein.	cDNA, clone: J075142E09, full insert sequence.	0.432
A0A0P0V1T6	A0A0N7KF42	A0A0P0V1T6	A0A0N7KF42	Os01g0314700 protein.	Os02g0288400 protein.	0.717
A0A0P0V1T6	A0A0P0VHR5	A0A0P0V1T6	A0A0P0VHR5	Os01g0314700 protein.	Os02g0288700 protein.	0.724
A0A0P0V1T6	A0A0P0WF03	A0A0P0V1T6	A0A0P0WF03	Os01g0314700 protein.	Os04g0620066 protein.	0.717
A0A0P0V1T6	A0A0P0YBE6	A0A0P0V1T6	A0A0P0YBE6	Os01g0314700 protein.	Os12g0562700 protein.	0.717
A0A0P0V1T6	Q0JA19_ORYSJ	A0A0P0V1T6	Q0JA19	Os01g0314700 protein.	Os04g0620000 protein.	0.717
A0A0P0V1T6	Q0JES2_ORYSJ	A0A0P0V1T6	Q0JES2	Os01g0314700 protein.	Os04g0209200 protein.	0.717
A0A0P0V1T6	Q6Z9U8_ORYSJ	A0A0P0V1T6	Q6Z9U8	Os01g0314700 protein.	Os08g0179900 protein.	0.717
A0A0P0V1T6	Q7XM41_ORYSJ	A0A0P0V1T6	Q7XM41	Os01g0314700 protein.	cDNA clone:J013026A05, full insert sequence.	0.717
A0A0P0V1T6	mrp8	A0A0P0V1T6	Q8GU64	Os01g0314700 protein.	cDNA, clone: J075142E09, full insert sequence.	0.717
A0A0P0VHR5	A0A0P0V1T6	A0A0P0VHR5	A0A0P0V1T6	Os02g0288700 protein.	Os01g0314700 protein.	0.724
A0A0P0VHR5	A0A0P0WF03	A0A0P0VHR5	A0A0P0WF03	Os02g0288700 protein.	Os04g0620066 protein.	0.461
A0A0P0VHR5	A0A0P0YBE6	A0A0P0VHR5	A0A0P0YBE6	Os02g0288700 protein.	Os12g0562700 protein.	0.663
A0A0P0VHR5	Q0D3X3_ORYSJ	A0A0P0VHR5	Q0D3X3	Os02g0288700 protein.	Ubiquitin carboxyl-terminal hydrolase; Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Belongs to the peptidase C19 family.	0.677

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Network Stats

number of nodes:

6

number of edges:

8

average node degree:

2.67

avg. local clustering coefficient:

0.883

expected number of edges:

6

PPI enrichment p-value:

0.223

your network does not have 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:0006289

Nucleotide-excision repair

4 of 39

2.18

2.21

4.69e-05

GO:0000724

Double-strand break repair via homologous recombination

4 of 67

1.95

1.84

0.00018

GO:0006261

DNA-templated DNA replication

4 of 105

1.75

1.57

0.00044

GO:0007004

Telomere maintenance via telomerase

2 of 8

2.57

1.27

0.0048

GO:0022402

Cell cycle process

5 of 338

1.34

1.19

0.00072

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003684

Damaged DNA binding

3 of 27

2.22

1.51

0.0014

GO:0003697

Single-stranded DNA binding

3 of 36

2.09

1.45

0.0016

GO:0043047

Single-stranded telomeric DNA binding

2 of 6

2.69

1.22

0.0061

GO:0003677

DNA binding

5 of 796

0.97

0.57

0.0266

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030894

Replisome

4 of 14

2.63

3.49

2.67e-07

GO:0005662

DNA replication factor A complex

3 of 3

3.17

1.79e-06

GO:0000228

Nuclear chromosome

4 of 114

1.72

1.8

9.23e-05

GO:0000781

Chromosome, telomeric region

3 of 47

1.98

1.73

0.00034

GO:0005694

Chromosome

5 of 415

1.25

1.18

0.00034

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:11570

DNA-templated DNA replication, and DNA Double-Strand Break Repair

7 of 169

1.79

3.13

9.93e-09

CL:11577

Mixed, incl. HDR through Homologous Recombination (HRR), and DNA strand elongation

5 of 96

1.89

2.52

2.56e-06

CL:11587

HDR through Homologous Recombination (HRR), and DNA damage checkpoint signaling

4 of 54

2.04

2.34

1.62e-05

CL:11599

HDR through Single Strand Annealing (SSA), and Sensing of DNA Double Strand Breaks

3 of 24

2.27

1.97

0.00017

CL:11637

DNA replication factor A complex, and RecQ family helicase-topoisomerase III complex

2 of 5

2.77

1.55

0.0015

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03420

Nucleotide excision repair

8 of 153

1.89

4.38

1.82e-12

map03430

Mismatch repair

7 of 140

1.87

3.87

1.00e-10

map03030

DNA replication

7 of 164

1.8

3.61

1.95e-10

map03440

Homologous recombination

7 of 184

1.75

3.42

3.21e-10

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-5696395

Formation of Incision Complex in GG-NER

3 of 31

2.16

1.81

0.00032

MAP-6781827

Transcription-Coupled Nucleotide Excision Repair (TC-NER)

5 of 172

1.64

1.79

5.83e-05

MAP-5696398

Nucleotide Excision Repair

5 of 199

1.57

1.72

5.93e-05

MAP-5358606

Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)

2 of 7

2.63

1.68

0.00082

MAP-5696400

Dual Incision in GG-NER

4 of 117

1.71

1.61

0.00029

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005662

DNA replication factor A complex

3 of 5

2.95

2.69

1.22e-05

GOCC:0000228

Nuclear chromosome

4 of 164

1.56

1.41

0.00054

GOCC:0005634

Nucleus

7 of 1487

0.84

0.68

0.0015

GOCC:0032991

Protein-containing complex

9 of 2717

0.69

0.57

0.00054

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF08784

Replication protein A C terminal

2 of 2

3.17

1.44

0.0025

PF01336

OB-fold nucleic acid binding domain

2 of 7

2.63

1.17

0.0075

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR040260

Replication factor A protein-like

3 of 3

3.17

2.69

1.32e-05

IPR012340

Nucleic acid-binding, OB-fold

4 of 61

1.99

1.95

0.00011

IPR014892

Replication protein A, C-terminal

2 of 2

3.17

1.45

0.0024

IPR004365

OB-fold nucleic acid binding domain, AA-tRNA synthetase-type

2 of 8

2.57

1.03

0.0135

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