(13 nodes) Nonfunctional rRNA decay network (Verticillium alfalfae)

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.

Node Color

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:
	VDBG_03968	Uncharacterized protein. (287 aa)
	VDBG_00759	Thermotolerance protein. (1315 aa)
	VDBG_02195	Exosome complex exonuclease RRP43. (340 aa)
	VDBG_03613	3'-5' exonuclease domain-containing protein. (894 aa)
	VDBG_03680	RNase_PH domain-containing protein. (373 aa)
	VDBG_04642	NPL4. (250 aa)
	VDBG_04644	NPL4. (342 aa)
	VDBG_05197	Ubiquitin fusion degradation protein. (374 aa)
	VDBG_05506	Proteasome 19S regulatory particle. (93 aa)
	VDBG_05847	RNase_PH domain-containing protein. (249 aa)
	VDBG_06740	Exosome complex exonuclease RRP45. (271 aa)
	VDBG_07792	Protein DOM34 homolog; May function in recognizing stalled ribosomes and triggering endonucleolytic cleavage of the mRNA, a mechanism to release non- functional ribosomes and degrade damaged mRNAs. (398 aa)
	VDBG_09932	Exosome complex exonuclease RRP41. (155 aa)

Your Current Organism:

Verticillium alfalfae

NCBI taxonomy Id: 526221
Other names: V. alfalfae VaMs.102, Verticillium alfalfae VaMs.102

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

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

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
VDBG_02195	VDBG_03613	C9S9M3	C9SGG4	Exosome complex exonuclease RRP43.	3'-5' exonuclease domain-containing protein.	0.962
VDBG_02195	VDBG_03680	C9S9M3	C9SGU9	Exosome complex exonuclease RRP43.	RNase_PH domain-containing protein.	0.999
VDBG_02195	VDBG_05847	C9S9M3	C9SLS3	Exosome complex exonuclease RRP43.	RNase_PH domain-containing protein.	0.999
VDBG_02195	VDBG_06740	C9S9M3	C9SPB5	Exosome complex exonuclease RRP43.	Exosome complex exonuclease RRP45.	0.999
VDBG_02195	VDBG_09932	C9S9M3	C9SYF7	Exosome complex exonuclease RRP43.	Exosome complex exonuclease RRP41.	0.999
VDBG_03613	VDBG_02195	C9SGG4	C9S9M3	3'-5' exonuclease domain-containing protein.	Exosome complex exonuclease RRP43.	0.962
VDBG_03613	VDBG_05506	C9SGG4	C9SL29	3'-5' exonuclease domain-containing protein.	Proteasome 19S regulatory particle.	0.544
VDBG_03680	VDBG_02195	C9SGU9	C9S9M3	RNase_PH domain-containing protein.	Exosome complex exonuclease RRP43.	0.999
VDBG_03680	VDBG_05847	C9SGU9	C9SLS3	RNase_PH domain-containing protein.	RNase_PH domain-containing protein.	0.997
VDBG_03680	VDBG_06740	C9SGU9	C9SPB5	RNase_PH domain-containing protein.	Exosome complex exonuclease RRP45.	0.999
VDBG_03680	VDBG_09932	C9SGU9	C9SYF7	RNase_PH domain-containing protein.	Exosome complex exonuclease RRP41.	0.998
VDBG_04642	VDBG_04644	C9SHW0	C9SHW2	NPL4.	NPL4.	0.993
VDBG_04642	VDBG_05197	C9SHW0	C9SK70	NPL4.	Ubiquitin fusion degradation protein.	0.996
VDBG_04642	VDBG_05506	C9SHW0	C9SL29	NPL4.	Proteasome 19S regulatory particle.	0.509
VDBG_04644	VDBG_04642	C9SHW2	C9SHW0	NPL4.	NPL4.	0.993
VDBG_04644	VDBG_05197	C9SHW2	C9SK70	NPL4.	Ubiquitin fusion degradation protein.	0.996
VDBG_04644	VDBG_05506	C9SHW2	C9SL29	NPL4.	Proteasome 19S regulatory particle.	0.509
VDBG_05197	VDBG_04642	C9SK70	C9SHW0	Ubiquitin fusion degradation protein.	NPL4.	0.996
VDBG_05197	VDBG_04644	C9SK70	C9SHW2	Ubiquitin fusion degradation protein.	NPL4.	0.996
VDBG_05197	VDBG_05506	C9SK70	C9SL29	Ubiquitin fusion degradation protein.	Proteasome 19S regulatory particle.	0.731