(11 nodes) mRNA surveillance pathway, and HDACs deacetylate histones network (Cavenderia fasciculata)

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:
	DFA_03263	Uncharacterized protein. (671 aa)
	magoh	Mago nashi protein. (176 aa)
	uap56	DEAD/DEAH box helicase. (426 aa)
	DFA_04683	RNA-binding region RNP-1 domain-containing protein. (348 aa)
	pabpn1	Polyadenylate-binding protein 2. (243 aa)
	tifA	DEAD/DEAH box helicase domain-containing protein; Belongs to the DEAD box helicase family. (418 aa)
	rbm8A	RNA recognition motif-containing protein RRM. (211 aa)
	DFA_01769	Smg4_UPF3 domain-containing protein. (206 aa)
	DFA_07562	SAP DNA-binding domain-containing protein. (633 aa)
	srrm1	Putative RNA splicing factor. (534 aa)
	DFA_07615	Pinin_SDK_memA domain-containing protein. (422 aa)

Your Current Organism:

Cavenderia fasciculata

NCBI taxonomy Id: 1054147
Other names: C. fasciculata SH3, Cavenderia fasciculata SH3, Dictyostelium fasciculatum SH3, Dictyostelium fasciculatum strain SH3

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
DFA_01769	DFA_03263	F4PUL9	F4PH33	Smg4_UPF3 domain-containing protein.	Uncharacterized protein.	0.719
DFA_01769	DFA_04683	F4PUL9	F4PQ90	Smg4_UPF3 domain-containing protein.	RNA-binding region RNP-1 domain-containing protein.	0.968
DFA_01769	DFA_07562	F4PUL9	F4PWS4	Smg4_UPF3 domain-containing protein.	SAP DNA-binding domain-containing protein.	0.673
DFA_01769	DFA_07615	F4PUL9	F4Q651	Smg4_UPF3 domain-containing protein.	Pinin_SDK_memA domain-containing protein.	0.815
DFA_01769	magoh	F4PUL9	F4PN54	Smg4_UPF3 domain-containing protein.	Mago nashi protein.	0.965
DFA_01769	pabpn1	F4PUL9	F4PQQ4	Smg4_UPF3 domain-containing protein.	Polyadenylate-binding protein 2.	0.959
DFA_01769	rbm8A	F4PUL9	F4PTU0	Smg4_UPF3 domain-containing protein.	RNA recognition motif-containing protein RRM.	0.982
DFA_01769	srrm1	F4PUL9	F4Q172	Smg4_UPF3 domain-containing protein.	Putative RNA splicing factor.	0.979
DFA_01769	tifA	F4PUL9	F4PT25	Smg4_UPF3 domain-containing protein.	DEAD/DEAH box helicase domain-containing protein; Belongs to the DEAD box helicase family.	0.986
DFA_01769	uap56	F4PUL9	F4PP34	Smg4_UPF3 domain-containing protein.	DEAD/DEAH box helicase.	0.883
DFA_03263	DFA_01769	F4PH33	F4PUL9	Uncharacterized protein.	Smg4_UPF3 domain-containing protein.	0.719
DFA_03263	DFA_04683	F4PH33	F4PQ90	Uncharacterized protein.	RNA-binding region RNP-1 domain-containing protein.	0.754
DFA_03263	DFA_07562	F4PH33	F4PWS4	Uncharacterized protein.	SAP DNA-binding domain-containing protein.	0.990
DFA_03263	DFA_07615	F4PH33	F4Q651	Uncharacterized protein.	Pinin_SDK_memA domain-containing protein.	0.963
DFA_03263	magoh	F4PH33	F4PN54	Uncharacterized protein.	Mago nashi protein.	0.882
DFA_03263	pabpn1	F4PH33	F4PQQ4	Uncharacterized protein.	Polyadenylate-binding protein 2.	0.978
DFA_03263	rbm8A	F4PH33	F4PTU0	Uncharacterized protein.	RNA recognition motif-containing protein RRM.	0.877
DFA_03263	srrm1	F4PH33	F4Q172	Uncharacterized protein.	Putative RNA splicing factor.	0.739
DFA_03263	tifA	F4PH33	F4PT25	Uncharacterized protein.	DEAD/DEAH box helicase domain-containing protein; Belongs to the DEAD box helicase family.	0.878
DFA_03263	uap56	F4PH33	F4PP34	Uncharacterized protein.	DEAD/DEAH box helicase.	0.532