PCDH20 protein (Latimeria chalumnae) - STRING interaction network

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.

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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

PCDH20

Uncharacterized protein. (875 aa)

Predicted Functional Partners:

H2ZY56_LATCH

0.900

LOC102365358

0.669

AGA

0.598

GNPNAT1

0.579

B3GNT7

0.538

SCAPER

0.422

Your Current Organism:

Latimeria chalumnae

NCBI taxonomy Id: 7897
Other names: L. chalumnae, coelacanth

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
AGA	B3GNT7	ENSLACP00000002066	ENSLACP00000006013	Aspartylglucosaminidase.	Hexosyltransferase.	0.522
AGA	GNPNAT1	ENSLACP00000002066	ENSLACP00000021741	Aspartylglucosaminidase.	Glucosamine 6-phosphate N-acetyltransferase.	0.588
AGA	LOC102365358	ENSLACP00000002066	ENSLACP00000021719	Aspartylglucosaminidase.	Hexosyltransferase.	0.658
AGA	PCDH20	ENSLACP00000002066	ENSLACP00000012149	Aspartylglucosaminidase.	Uncharacterized protein.	0.598
B3GNT7	AGA	ENSLACP00000006013	ENSLACP00000002066	Hexosyltransferase.	Aspartylglucosaminidase.	0.522
B3GNT7	GNPNAT1	ENSLACP00000006013	ENSLACP00000021741	Hexosyltransferase.	Glucosamine 6-phosphate N-acetyltransferase.	0.511
B3GNT7	LOC102365358	ENSLACP00000006013	ENSLACP00000021719	Hexosyltransferase.	Hexosyltransferase.	0.902
B3GNT7	PCDH20	ENSLACP00000006013	ENSLACP00000012149	Hexosyltransferase.	Uncharacterized protein.	0.538
GNPNAT1	AGA	ENSLACP00000021741	ENSLACP00000002066	Glucosamine 6-phosphate N-acetyltransferase.	Aspartylglucosaminidase.	0.588
GNPNAT1	B3GNT7	ENSLACP00000021741	ENSLACP00000006013	Glucosamine 6-phosphate N-acetyltransferase.	Hexosyltransferase.	0.511
GNPNAT1	LOC102365358	ENSLACP00000021741	ENSLACP00000021719	Glucosamine 6-phosphate N-acetyltransferase.	Hexosyltransferase.	0.651
GNPNAT1	PCDH20	ENSLACP00000021741	ENSLACP00000012149	Glucosamine 6-phosphate N-acetyltransferase.	Uncharacterized protein.	0.579
H2ZY56_LATCH	PCDH20	ENSLACP00000002327	ENSLACP00000012149	Uncharacterized protein.	Uncharacterized protein.	0.900
LOC102365358	AGA	ENSLACP00000021719	ENSLACP00000002066	Hexosyltransferase.	Aspartylglucosaminidase.	0.658
LOC102365358	B3GNT7	ENSLACP00000021719	ENSLACP00000006013	Hexosyltransferase.	Hexosyltransferase.	0.902
LOC102365358	GNPNAT1	ENSLACP00000021719	ENSLACP00000021741	Hexosyltransferase.	Glucosamine 6-phosphate N-acetyltransferase.	0.651
LOC102365358	PCDH20	ENSLACP00000021719	ENSLACP00000012149	Hexosyltransferase.	Uncharacterized protein.	0.669
PCDH20	AGA	ENSLACP00000012149	ENSLACP00000002066	Uncharacterized protein.	Aspartylglucosaminidase.	0.598
PCDH20	B3GNT7	ENSLACP00000012149	ENSLACP00000006013	Uncharacterized protein.	Hexosyltransferase.	0.538
PCDH20	GNPNAT1	ENSLACP00000012149	ENSLACP00000021741	Uncharacterized protein.	Glucosamine 6-phosphate N-acetyltransferase.	0.579

page 1 of 2

Network Stats

number of nodes:

9

number of edges:

15

average node degree:

3.33

avg. local clustering coefficient:

0.917

expected number of edges:

11

PPI enrichment p-value:

0.157

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:0060563

Neuroepithelial cell differentiation

3 of 9

3.07

2.79

2.69e-05

GO:0040036

Regulation of fibroblast growth factor receptor signaling pathway

3 of 31

2.53

2.05

0.00036

GO:0110148

Biomineralization

3 of 49

2.33

1.79

0.00090

GO:0030433

Ubiquitin-dependent ERAD pathway

3 of 72

2.17

1.61

0.0016

GO:0036035

Osteoclast development

2 of 8

2.94

1.53

0.0032

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005509

Calcium ion binding

7 of 822

1.48

2.17

3.93e-07

GO:0030145

Manganese ion binding

3 of 59

2.25

1.81

0.00076

GO:0051082

Unfolded protein binding

3 of 117

1.96

1.48

0.0022

GO:0016773

Phosphotransferase activity, alcohol group as acceptor

4 of 927

1.18

0.68

0.0288

GO:0016301

Kinase activity

4 of 1004

1.15

0.65

0.0343

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005788

Endoplasmic reticulum lumen

4 of 89

2.2

2.76

9.76e-06

GO:0005794

Golgi apparatus

5 of 1252

1.15

0.9

0.0037

GO:0005635

Nuclear envelope

3 of 296

1.55

0.89

0.0201

GO:0012505

Endomembrane system

8 of 3682

0.88

0.83

5.46e-05

GO:0005789

Endoplasmic reticulum membrane

4 of 958

1.17

0.72

0.0215

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:20628614

(2010) Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species.

3 of 4

3.42

3.44

2.52e-06

PMID:33199536

(2020) Mannose-Binding Lectin Possesses Agglutination Activity and Promotes Opsonophagocytosis of Macrophages with Calreticulin Interaction in an Early Vertebrate.

3 of 5

3.32

3.43

2.52e-06

PMID:28254621

(2017) Nutrigenomics and immune function in fish: new insights from omics technologies.

3 of 6

3.25

3.43

2.52e-06

PMID:24060503

(2014) Rainbow trout (Oncorhynchus mykiss) contain two calnexin genes which encode distinct proteins.

3 of 7

3.18

3.42

2.52e-06

PMID:35153391

(2022) Molecular cloning, sequence characterization, and expression analysis of C-type lectin (CTL) and ER-Golgi intermediate compartment 53-kDa protein (ERGIC-53) homologs from the freshwater prawn, Macrobrachium rosenbergii.

3 of 8

3.12

3.41

2.52e-06

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:34412

Mixed, incl. FAM20, C-terminal, and Flavin-linked sulfhydryl oxidase activity

4 of 11

3.11

4.65

2.11e-08

CL:39427

Calreticulin, and Protein disulphide isomerase

3 of 6

3.25

3.62

1.22e-06

CL:34416

FAM20, C-terminal, and Flavin-linked sulfhydryl oxidase activity

3 of 6

3.25

3.62

1.22e-06

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

onl04141

Protein processing in endoplasmic reticulum

3 of 179

1.77

1.38

0.0024

onl04145

Phagosome

3 of 210

1.7

1.35

0.0024

onl05168

Herpes simplex virus 1 infection

3 of 342

1.49

1.09

0.0054

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-3000480

Scavenging by Class A Receptors

3 of 11

2.98

3.06

9.12e-06

MAP-901042

Calnexin/calreticulin cycle

3 of 33

2.5

2.6

3.85e-05

MAP-532668

N-glycan trimming in the ER and Calnexin/Calreticulin cycle

3 of 45

2.37

2.44

6.16e-05

MAP-8957275

Post-translational protein phosphorylation

4 of 168

1.92

2.27

3.85e-05

MAP-381426

Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

4 of 199

1.85

2.15

4.99e-05

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005788

Endoplasmic reticulum lumen

4 of 56

2.4

3.24

2.01e-06

GOCC:0012505

Endomembrane system

8 of 2410

1.07

1.21

2.27e-06

GOCC:0005794

Golgi apparatus

4 of 581

1.38

1.01

0.0062

GOCC:0005737

Cytoplasm

8 of 6894

0.61

0.44

0.0062

GOCC:0043231

Intracellular membrane-bounded organelle

8 of 7225

0.59

0.43

0.0062

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0143

Chaperone

3 of 26

2.61

2.81

1.82e-05

KW-0256

Endoplasmic reticulum

3 of 108

1.99

1.79

0.00055

KW-0106

Calcium

4 of 429

1.52

1.46

0.00055

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF06702

Golgi casein kinase, C-terminal, Fam20

4 of 6

3.37

5.42

1.34e-09

PF00262

Calreticulin family

3 of 5

3.32

3.68

1.00e-06

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR009169

Calreticulin

3 of 3

3.55

3.53

1.84e-06

IPR024869

FAM20

3 of 5

3.32

3.43

2.57e-06

IPR018124

Calreticulin/calnexin, conserved site

3 of 5

3.32

3.43

2.57e-06

IPR009581

FAM20, C-terminal

3 of 5

3.32

3.43

2.57e-06

IPR009033

Calreticulin/calnexin, P domain superfamily

3 of 5

3.32

3.43

2.57e-06

(more ...)

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