MA16_Dca002463 protein (Dendrobium catenatum)

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

MA16_Dca002463

Uncharacterized protein. (214 aa)

Predicted Functional Partners:

MA16_Dca002134

0.807

Mut11-6

0.658

Mut11-17

0.658

MA16_Dca001083

0.635

MBB1

0.616

MBB1-3

0.613

MA16_Dca000035

0.610

MA16_Dca023288

0.604

MA16_Dca013773

0.588

MA16_Dca012419

0.575

Your Current Organism:

Dendrobium catenatum

NCBI taxonomy Id: 906689
Other names: D. catenatum

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... functional annotations:

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a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
MA16_Dca000035	MA16_Dca001083	A0A2I0WSQ2	A0A2I0WLE3	U2 small nuclear ribonucleoprotein A.	Elongation factor 2.	0.976
MA16_Dca000035	MA16_Dca002134	A0A2I0WSQ2	A0A2I0XEH8	U2 small nuclear ribonucleoprotein A.	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase.	0.994
MA16_Dca000035	MA16_Dca002463	A0A2I0WSQ2	A0A2I0W0K2	U2 small nuclear ribonucleoprotein A.	Uncharacterized protein.	0.610
MA16_Dca000035	MA16_Dca012419	A0A2I0WSQ2	A0A2I0WYB8	U2 small nuclear ribonucleoprotein A.	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase.	0.972
MA16_Dca000035	MA16_Dca013773	A0A2I0WSQ2	A0A2I0VWF5	U2 small nuclear ribonucleoprotein A.	SKIP_SNW domain-containing protein.	0.971
MA16_Dca000035	MA16_Dca023288	A0A2I0WSQ2	A0A2I0X637	U2 small nuclear ribonucleoprotein A.	MPN domain-containing protein.	0.974
MA16_Dca000035	MBB1	A0A2I0WSQ2	A0A2I0WHI8	U2 small nuclear ribonucleoprotein A.	PsbB mRNA maturation factor Mbb1, chloroplastic.	0.977
MA16_Dca000035	MBB1-3	A0A2I0WSQ2	A0A2I0X6W4	U2 small nuclear ribonucleoprotein A.	PsbB mRNA maturation factor Mbb1, chloroplastic.	0.953
MA16_Dca000035	Mut11-17	A0A2I0WSQ2	A0A2I0X864	U2 small nuclear ribonucleoprotein A.	Protein Mut11.	0.915
MA16_Dca000035	Mut11-6	A0A2I0WSQ2	A0A2I0VMF1	U2 small nuclear ribonucleoprotein A.	Protein Mut11.	0.915
MA16_Dca001083	MA16_Dca000035	A0A2I0WLE3	A0A2I0WSQ2	Elongation factor 2.	U2 small nuclear ribonucleoprotein A.	0.976
MA16_Dca001083	MA16_Dca002134	A0A2I0WLE3	A0A2I0XEH8	Elongation factor 2.	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase.	0.978
MA16_Dca001083	MA16_Dca002463	A0A2I0WLE3	A0A2I0W0K2	Elongation factor 2.	Uncharacterized protein.	0.635
MA16_Dca001083	MA16_Dca012419	A0A2I0WLE3	A0A2I0WYB8	Elongation factor 2.	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase.	0.973
MA16_Dca001083	MA16_Dca013773	A0A2I0WLE3	A0A2I0VWF5	Elongation factor 2.	SKIP_SNW domain-containing protein.	0.976
MA16_Dca001083	MA16_Dca023288	A0A2I0WLE3	A0A2I0X637	Elongation factor 2.	MPN domain-containing protein.	0.997
MA16_Dca001083	MBB1	A0A2I0WLE3	A0A2I0WHI8	Elongation factor 2.	PsbB mRNA maturation factor Mbb1, chloroplastic.	0.980
MA16_Dca001083	MBB1-3	A0A2I0WLE3	A0A2I0X6W4	Elongation factor 2.	PsbB mRNA maturation factor Mbb1, chloroplastic.	0.980
MA16_Dca001083	Mut11-17	A0A2I0WLE3	A0A2I0X864	Elongation factor 2.	Protein Mut11.	0.921
MA16_Dca001083	Mut11-6	A0A2I0WLE3	A0A2I0VMF1	Elongation factor 2.	Protein Mut11.	0.921

page 1 of 6

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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