pdam_00008679 protein (Pocillopora damicornis)

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

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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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Gene Fusion

Cooccurrence

Coexpression

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[Homology]

Score

pdam_00008679

TPR_REGION domain-containing protein. (1351 aa)

Predicted Functional Partners:

pdam_00009858

0.809

pdam_00007959

0.474

pdam_00023782

0.474

pdam_00010727

0.453

pdam_00005907

0.449

pdam_00001602

0.447

pdam_00015958

0.445

pdam_00015045

0.441

pdam_00010580

0.441

pdam_00017461

0.440

Your Current Organism:

Pocillopora damicornis

NCBI taxonomy Id: 46731
Other names: P. damicornis, Pocillopora caespitosa laysanensis, Pocillopora damicornis laysanensis, cauliflower coral, lace coral

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
pdam_00001602	pdam_00005907	A0A3M6U5A5	A0A3M6TBC0	WD_REPEATS_REGION domain-containing protein.	TPR_REGION domain-containing protein.	0.999
pdam_00001602	pdam_00007959	A0A3M6U5A5	A0A3M6UF74	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.560
pdam_00001602	pdam_00008679	A0A3M6U5A5	A0A3M6TFV8	WD_REPEATS_REGION domain-containing protein.	TPR_REGION domain-containing protein.	0.447
pdam_00001602	pdam_00015958	A0A3M6U5A5	A0A3M6THA3	WD_REPEATS_REGION domain-containing protein.	APC1_C domain-containing protein.	0.999
pdam_00001602	pdam_00017461	A0A3M6U5A5	A0A3M6UQW3	WD_REPEATS_REGION domain-containing protein.	ANAPC5 domain-containing protein.	0.999
pdam_00001602	pdam_00023782	A0A3M6U5A5	A0A3M6UXX2	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.560
pdam_00005907	pdam_00001602	A0A3M6TBC0	A0A3M6U5A5	TPR_REGION domain-containing protein.	WD_REPEATS_REGION domain-containing protein.	0.999
pdam_00005907	pdam_00007959	A0A3M6TBC0	A0A3M6UF74	TPR_REGION domain-containing protein.	Uncharacterized protein.	0.556
pdam_00005907	pdam_00008679	A0A3M6TBC0	A0A3M6TFV8	TPR_REGION domain-containing protein.	TPR_REGION domain-containing protein.	0.449
pdam_00005907	pdam_00015958	A0A3M6TBC0	A0A3M6THA3	TPR_REGION domain-containing protein.	APC1_C domain-containing protein.	0.999
pdam_00005907	pdam_00017461	A0A3M6TBC0	A0A3M6UQW3	TPR_REGION domain-containing protein.	ANAPC5 domain-containing protein.	0.999
pdam_00005907	pdam_00023782	A0A3M6TBC0	A0A3M6UXX2	TPR_REGION domain-containing protein.	Uncharacterized protein.	0.556
pdam_00007959	pdam_00001602	A0A3M6UF74	A0A3M6U5A5	Uncharacterized protein.	WD_REPEATS_REGION domain-containing protein.	0.560
pdam_00007959	pdam_00005907	A0A3M6UF74	A0A3M6TBC0	Uncharacterized protein.	TPR_REGION domain-containing protein.	0.556
pdam_00007959	pdam_00008679	A0A3M6UF74	A0A3M6TFV8	Uncharacterized protein.	TPR_REGION domain-containing protein.	0.474
pdam_00007959	pdam_00009858	A0A3M6UF74	A0A3M6TLU0	Uncharacterized protein.	Uncharacterized protein.	0.984
pdam_00007959	pdam_00010727	A0A3M6UF74	A0A3M6UK08	Uncharacterized protein.	Uncharacterized protein.	0.689
pdam_00007959	pdam_00015958	A0A3M6UF74	A0A3M6THA3	Uncharacterized protein.	APC1_C domain-containing protein.	0.545
pdam_00007959	pdam_00017461	A0A3M6UF74	A0A3M6UQW3	Uncharacterized protein.	ANAPC5 domain-containing protein.	0.538
pdam_00008679	pdam_00001602	A0A3M6TFV8	A0A3M6U5A5	TPR_REGION domain-containing protein.	WD_REPEATS_REGION domain-containing protein.	0.447

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

17

average node degree:

3.09

avg. local clustering coefficient:

0.923

expected number of edges:

11

PPI enrichment p-value:

0.0526

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:0042273

Ribosomal large subunit biogenesis

7 of 129

1.95

3.9

3.64e-10

GO:0000463

Maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

5 of 48

2.23

3.62

3.87e-08

GO:0042254

Ribosome biogenesis

11 of 536

1.52

3.19

8.87e-14

GO:0030490

Maturation of SSU-rRNA

6 of 125

1.89

3.19

3.08e-08

GO:0006364

rRNA processing

9 of 400

1.56

2.93

1.24e-10

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030515

snoRNA binding

4 of 45

2.16

2.38

1.87e-05

GO:0003723

RNA binding

9 of 1125

1.11

1.31

1.81e-06

GO:0042134

rRNA primary transcript binding

2 of 12

2.43

0.95

0.0181

GO:0003724

RNA helicase activity

3 of 113

1.64

0.84

0.0196

GO:0005488

Binding

11 of 7915

0.35

0.26

0.0422

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030689

Noc complex

4 of 8

2.91

4.46

5.53e-09

GO:0030684

Preribosome

8 of 178

1.86

4.12

9.52e-12

GO:0005730

Nucleolus

11 of 476

1.58

3.55

5.47e-15

GO:0030686

90S preribosome

4 of 56

2.07

2.64

3.42e-06

GO:0030687

Preribosome, large subunit precursor

4 of 59

2.04

2.6

3.82e-06

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:9923

Maturation of SSU-rRNA, and Small-subunit processome

6 of 131

1.87

2.85

2.52e-07

CL:9931

Small-subunit processome, and Endonucleolytic cleavage to generate mature 5-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

5 of 91

1.95

2.57

2.81e-06

CL:10188

Preribosome, large subunit precursor, and Maturation of LSU-rRNA

5 of 95

1.93

2.56

2.81e-06

CL:10205

Preribosome, large subunit precursor, and Nop2p

4 of 47

2.14

2.55

7.42e-06

CL:9940

Small-subunit processome

4 of 74

1.94

2.19

2.59e-05

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-6791226

Major pathway of rRNA processing in the nucleolus and cytosol

8 of 257

1.7

3.28

3.28e-10

MAP-8868773

rRNA processing in the nucleus and cytosol

8 of 263

1.69

3.25

3.28e-10

MAP-72312

rRNA processing

8 of 272

1.68

3.21

3.28e-10

MAP-8953854

Metabolism of RNA

8 of 1097

1.07

1.19

7.15e-06

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0030684

Preribosome

8 of 153

1.93

4.35

7.47e-12

GOCC:0030686

90S preribosome

6 of 62

2.2

4.29

7.04e-10

GOCC:0030689

Noc complex

4 of 12

2.73

3.86

6.02e-08

GOCC:0030691

Noc2p-Noc3p complex

2 of 4

2.91

1.63

0.0011

GOCC:0030690

Noc1p-Noc2p complex

2 of 4

2.91

1.63

0.0011

(more ...)

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF06732

Pescadillo N-terminus

2 of 2

3.21

1.25

0.0057

PF04147

Nop14-like family

2 of 2

3.21

1.25

0.0057

PF03715

Noc2p family

2 of 2

3.21

1.25

0.0057

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR045209

rRNA biogenesis protein Rrp5

2 of 2

3.21

1.01

0.0151

IPR010613

Pescadillo

2 of 2

3.21

1.01

0.0151

IPR007276

Nucleolar protein 14

2 of 2

3.21

1.01

0.0151

IPR005343

Nucleolar complex protein 2

2 of 2

3.21

1.01

0.0151

IPR011545

DEAD/DEAH box helicase domain

3 of 88

1.74

0.78

0.0299

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00316

Ribosomal protein S1-like RNA-binding domain

2 of 14

2.37

0.9

0.0228

SM00386

HAT (Half-A-TPR) repeats

2 of 16

2.31

0.89

0.0228

SM00490

Helicase superfamily c-terminal domain

3 of 149

1.52

0.79

0.0228

SM00487

DEAD-like helicases superfamily

3 of 152

1.51

0.78

0.0228

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