(13 nodes) Formation of RNA Pol II elongation complex network (Xiphophorus couchianus)

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:
	ENSXCOP00000026128	Negative elongation factor complex member E. (330 aa)
	ENSXCOP00000000267	Cyclin-dependent kinase 9 (CDC2-related kinase). (379 aa)
	ELOB	Elongin B. (126 aa)
	ENSXCOP00000002330	Uncharacterized protein. (384 aa)
	Gtf2h4	General transcription factor IIH subunit 4; Component of the general transcription and DNA repair factor IIH (TFIIH) core complex which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA. Belongs to the TFB2 family. (447 aa)
	ENSXCOP00000005151	RTF1 homolog, Paf1/RNA polymerase II complex component. (668 aa)
	Nelfa	Negative elongation factor complex member A. (525 aa)
	CCNT2	Cyclin T2; Belongs to the cyclin family. (626 aa)
	ENSXCOP00000019505	Uncharacterized protein. (290 aa)
	POLR2B	RNA polymerase II subunit B. (366 aa)
	polr2f	Polymerase (RNA) II (DNA directed) polypeptide F. (127 aa)
	ENSXCOP00000023376	Cyclin T2b; Belongs to the cyclin family. (511 aa)
	ENSXCOP00000024151	Elongin B. (117 aa)

Your Current Organism:

Xiphophorus couchianus

NCBI taxonomy Id: 32473
Other names: Limia couchiana, Monterrey platyfish, X. couchianus

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
CCNT2	ELOB	ENSXCOP00000019303	ENSXCOP00000001255	Cyclin T2; Belongs to the cyclin family.	Elongin B.	0.489
CCNT2	ENSXCOP00000000267	ENSXCOP00000019303	ENSXCOP00000000267	Cyclin T2; Belongs to the cyclin family.	Cyclin-dependent kinase 9 (CDC2-related kinase).	0.946
CCNT2	ENSXCOP00000002330	ENSXCOP00000019303	ENSXCOP00000002330	Cyclin T2; Belongs to the cyclin family.	Uncharacterized protein.	0.776
CCNT2	ENSXCOP00000019505	ENSXCOP00000019303	ENSXCOP00000019505	Cyclin T2; Belongs to the cyclin family.	Uncharacterized protein.	0.489
CCNT2	ENSXCOP00000024151	ENSXCOP00000019303	ENSXCOP00000024151	Cyclin T2; Belongs to the cyclin family.	Elongin B.	0.489
CCNT2	ENSXCOP00000026128	ENSXCOP00000019303	ENSXCOP00000026128	Cyclin T2; Belongs to the cyclin family.	Negative elongation factor complex member E.	0.715
CCNT2	Gtf2h4	ENSXCOP00000019303	ENSXCOP00000004365	Cyclin T2; Belongs to the cyclin family.	General transcription factor IIH subunit 4; Component of the general transcription and DNA repair factor IIH (TFIIH) core complex which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA. Belongs to the TFB2 family.	0.511
CCNT2	Nelfa	ENSXCOP00000019303	ENSXCOP00000011973	Cyclin T2; Belongs to the cyclin family.	Negative elongation factor complex member A.	0.548
CCNT2	POLR2B	ENSXCOP00000019303	ENSXCOP00000019507	Cyclin T2; Belongs to the cyclin family.	RNA polymerase II subunit B.	0.489
CCNT2	polr2f	ENSXCOP00000019303	ENSXCOP00000021360	Cyclin T2; Belongs to the cyclin family.	Polymerase (RNA) II (DNA directed) polypeptide F.	0.622
ELOB	CCNT2	ENSXCOP00000001255	ENSXCOP00000019303	Elongin B.	Cyclin T2; Belongs to the cyclin family.	0.489
ELOB	ENSXCOP00000000267	ENSXCOP00000001255	ENSXCOP00000000267	Elongin B.	Cyclin-dependent kinase 9 (CDC2-related kinase).	0.554
ELOB	ENSXCOP00000002330	ENSXCOP00000001255	ENSXCOP00000002330	Elongin B.	Uncharacterized protein.	0.452
ELOB	ENSXCOP00000023376	ENSXCOP00000001255	ENSXCOP00000023376	Elongin B.	Cyclin T2b; Belongs to the cyclin family.	0.489
ELOB	ENSXCOP00000024151	ENSXCOP00000001255	ENSXCOP00000024151	Elongin B.	Elongin B.	0.901
ELOB	ENSXCOP00000026128	ENSXCOP00000001255	ENSXCOP00000026128	Elongin B.	Negative elongation factor complex member E.	0.661
ELOB	polr2f	ENSXCOP00000001255	ENSXCOP00000021360	Elongin B.	Polymerase (RNA) II (DNA directed) polypeptide F.	0.589
ENSXCOP00000000267	CCNT2	ENSXCOP00000000267	ENSXCOP00000019303	Cyclin-dependent kinase 9 (CDC2-related kinase).	Cyclin T2; Belongs to the cyclin family.	0.946
ENSXCOP00000000267	ELOB	ENSXCOP00000000267	ENSXCOP00000001255	Cyclin-dependent kinase 9 (CDC2-related kinase).	Elongin B.	0.554
ENSXCOP00000000267	ENSXCOP00000002330	ENSXCOP00000000267	ENSXCOP00000002330	Cyclin-dependent kinase 9 (CDC2-related kinase).	Uncharacterized protein.	0.959