Phf3 protein (Oryzias latipes) - STRING interaction network

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

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a 3D structure is known or predicted

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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

Phf3

Uncharacterized protein. (475 aa)

Predicted Functional Partners:

ENSORLP00000041087

0.899

polr2a

0.845

POLR2E

0.791

nipbl

0.721

LOC101156754

0.721

polr2b

0.711

polr2c

0.706

polr2j

0.703

H2LC37_ORYLA

0.693

polr2g

0.693

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
ENSORLP00000041087	H2LC37_ORYLA	ENSORLP00000041087	ENSORLP00000003471	TFIIS central domain-containing protein.	Uncharacterized protein.	0.693
ENSORLP00000041087	LOC101156754	ENSORLP00000041087	ENSORLP00000009535	TFIIS central domain-containing protein.	Nipped-B protein.	0.721
ENSORLP00000041087	POLR2E	ENSORLP00000041087	ENSORLP00000019213	TFIIS central domain-containing protein.	RNA polymerase II subunit E.	0.791
ENSORLP00000041087	Phf3	ENSORLP00000041087	ENSORLP00000012756	TFIIS central domain-containing protein.	Uncharacterized protein.	0.899
ENSORLP00000041087	nipbl	ENSORLP00000041087	ENSORLP00000006855	TFIIS central domain-containing protein.	Nipped-B protein.	0.721
ENSORLP00000041087	polr2a	ENSORLP00000041087	ENSORLP00000038121	TFIIS central domain-containing protein.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.845
ENSORLP00000041087	polr2b	ENSORLP00000041087	ENSORLP00000025492	TFIIS central domain-containing protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.711
ENSORLP00000041087	polr2c	ENSORLP00000041087	ENSORLP00000018932	TFIIS central domain-containing protein.	Polymerase (RNA) II (DNA directed) polypeptide C.	0.706
ENSORLP00000041087	polr2g	ENSORLP00000041087	ENSORLP00000003930	TFIIS central domain-containing protein.	Polymerase (RNA) II (DNA directed) polypeptide G-like.	0.693
ENSORLP00000041087	polr2j	ENSORLP00000041087	ENSORLP00000030642	TFIIS central domain-containing protein.	Polymerase (RNA) II (DNA directed) polypeptide J.	0.703
H2LC37_ORYLA	ENSORLP00000041087	ENSORLP00000003471	ENSORLP00000041087	Uncharacterized protein.	TFIIS central domain-containing protein.	0.693
H2LC37_ORYLA	POLR2E	ENSORLP00000003471	ENSORLP00000019213	Uncharacterized protein.	RNA polymerase II subunit E.	0.999
H2LC37_ORYLA	Phf3	ENSORLP00000003471	ENSORLP00000012756	Uncharacterized protein.	Uncharacterized protein.	0.693
H2LC37_ORYLA	polr2a	ENSORLP00000003471	ENSORLP00000038121	Uncharacterized protein.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.999
H2LC37_ORYLA	polr2b	ENSORLP00000003471	ENSORLP00000025492	Uncharacterized protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.999
H2LC37_ORYLA	polr2c	ENSORLP00000003471	ENSORLP00000018932	Uncharacterized protein.	Polymerase (RNA) II (DNA directed) polypeptide C.	0.999
H2LC37_ORYLA	polr2g	ENSORLP00000003471	ENSORLP00000003930	Uncharacterized protein.	Polymerase (RNA) II (DNA directed) polypeptide G-like.	0.999
H2LC37_ORYLA	polr2j	ENSORLP00000003471	ENSORLP00000030642	Uncharacterized protein.	Polymerase (RNA) II (DNA directed) polypeptide J.	0.999
LOC101156754	ENSORLP00000041087	ENSORLP00000009535	ENSORLP00000041087	Nipped-B protein.	TFIIS central domain-containing protein.	0.721
LOC101156754	Phf3	ENSORLP00000009535	ENSORLP00000012756	Nipped-B protein.	Uncharacterized protein.	0.721

page 1 of 5

Network Stats

number of nodes:

11

number of edges:

52

average node degree:

9.45

avg. local clustering coefficient:

0.958

expected number of edges:

13

PPI enrichment p-value:

1.11e-16

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:0009073

Aromatic amino acid family biosynthetic process

7 of 14

2.2

4.77

4.05e-11

GO:0000162

Tryptophan biosynthetic process

4 of 4

2.5

3.23

7.12e-07

GO:0046417

Chorismate metabolic process

3 of 9

2.02

1.85

0.00020

GO:0008652

Cellular amino acid biosynthetic process

7 of 99

1.35

1.81

7.12e-07

GO:0019438

Aromatic compound biosynthetic process

10 of 203

1.19

1.71

2.70e-09

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016829

Lyase activity

6 of 121

1.2

1.08

0.00060

GO:0016835

Carbon-oxygen lyase activity

4 of 46

1.44

1.03

0.0042

GO:0004834

Tryptophan synthase activity

2 of 2

2.5

1.03

0.0133

GO:0004106

Chorismate mutase activity

2 of 2

2.5

1.03

0.0133

GO:0016836

Hydro-lyase activity

3 of 37

1.41

0.7

0.0319

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005737

Cytoplasm

10 of 1270

0.4

0.28

0.0388

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:30808357

(2019) Metabolic engineering of microorganisms for production of aromatic compounds.

4 of 8

2.2

2.52

1.05e-05

PMID:34584039

(2021) Recent Advances in Synthetic, Industrial and Biological Applications of Violacein and Its Heterologous Production.

2 of 2

2.5

1.07

0.0109

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1391

Aromatic amino acid biosynthesis, and Anthranilate synthase/para-aminobenzoate synthase like domain

10 of 15

2.32

7.99

3.90e-19

CL:1393

Tryptophan biosynthesis

5 of 6

2.42

4.23

4.38e-09

CL:1407

Chorismate metabolic process

3 of 7

2.13

1.88

0.00022

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

pha00400

Phenylalanine, tyrosine and tryptophan biosynthesis

8 of 18

2.15

5.67

5.08e-14

pha01230

Biosynthesis of amino acids

8 of 113

1.35

2.04

1.36e-08

pha00790

Folate biosynthesis

3 of 24

1.6

1.25

0.0018

pha01110

Biosynthesis of secondary metabolites

8 of 287

0.95

0.97

1.13e-05

pha01100

Metabolic pathways

8 of 632

0.6

0.46

0.0026

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0057

Aromatic amino acid biosynthesis

7 of 12

2.27

5.34

3.03e-12

KW-0822

Tryptophan biosynthesis

5 of 5

2.5

4.45

2.07e-09

KW-0456

Lyase

9 of 133

1.33

2.1

1.40e-09

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF04715

Anthranilate synthase component I, N terminal region

2 of 2

2.5

0.84

0.0299

PF00425

Chorismate binding enzyme

2 of 2

2.5

0.84

0.0299

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00830

Chorismate mutase type II

2 of 2

2.5

1.18

0.0068

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