(24 nodes) Positive regulation of transcription initiation from RNA polymerase II promoter network (Maylandia zebra)

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:
	taf13	TATA-box binding protein associated factor 13. (124 aa)
	LOC101469646	MADS-box domain-containing protein. (506 aa)
	LOC101477738	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor. (854 aa)
	dhx36	DEAH (Asp-Glu-Ala-His) box polypeptide 36. (1064 aa)
	gtf2a2	Transcription initiation factor IIA subunit 2; TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation; Belongs to the TFIIA subunit 2 family. (111 aa)
	LOC101467809	TAFH domain-containing protein. (683 aa)
	ercc6	Excision repair cross-complementation group 6. (1439 aa)
	taf12	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (164 aa)
	LOC101480906	TAFH domain-containing protein. (1096 aa)
	gtf2a1	General transcription factor IIA, 1. (385 aa)
	taf3	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto. (940 aa)
	nkx2-5	NK2 homeobox 5. (320 aa)
	ercc1	Excision repair cross-complementation group 1. (352 aa)
	SRF	Serum response factor. (618 aa)
	psmc6	Proteasome 26S subunit, ATPase 6; Belongs to the AAA ATPase family. (389 aa)
	ENSMZEP00005020489	MADS-box domain-containing protein. (477 aa)
	paxip1	PAX interacting (with transcription-activation domain) protein 1. (1099 aa)
	med1	Mediator of RNA polymerase II transcription subunit 1; Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. (1752 aa)
	taf6	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (638 aa)
	taf10	Transcription initiation factor TFIID subunit 10; TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors; Belongs to the TAF10 family. (186 aa)
	LOC101478385	Si:dkey-219c3.2. (944 aa)
	sub1	SUB1 regulator of transcription a. (125 aa)
	med14	Mediator of RNA polymerase II transcription subunit 14; Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. (1374 aa)
	TAF4	TATA-box binding protein associated factor 4. (859 aa)

Your Current Organism:

Maylandia zebra

NCBI taxonomy Id: 106582
Other names: M. zebra, Metriaclima zebra, Pseudotropheus zebra, zebra mbuna

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
ENSMZEP00005020489	nkx2-5	ENSMZEP00005020489	ENSMZEP00005011918	MADS-box domain-containing protein.	NK2 homeobox 5.	0.450
LOC101467809	LOC101477738	ENSMZEP00005004658	ENSMZEP00005001168	TAFH domain-containing protein.	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	0.636
LOC101467809	TAF4	ENSMZEP00005004658	ENSMZEP00005034783	TAFH domain-containing protein.	TATA-box binding protein associated factor 4.	0.616
LOC101467809	gtf2a1	ENSMZEP00005004658	ENSMZEP00005008243	TAFH domain-containing protein.	General transcription factor IIA, 1.	0.782
LOC101467809	gtf2a2	ENSMZEP00005004658	ENSMZEP00005004377	TAFH domain-containing protein.	Transcription initiation factor IIA subunit 2; TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation; Belongs to the TFIIA subunit 2 family.	0.840
LOC101467809	taf10	ENSMZEP00005004658	ENSMZEP00005027427	TAFH domain-containing protein.	Transcription initiation factor TFIID subunit 10; TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors; Belongs to the TAF10 family.	0.929
LOC101467809	taf12	ENSMZEP00005004658	ENSMZEP00005005141	TAFH domain-containing protein.	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor.	0.953
LOC101467809	taf13	ENSMZEP00005004658	ENSMZEP00005029636	TAFH domain-containing protein.	TATA-box binding protein associated factor 13.	0.929
LOC101467809	taf3	ENSMZEP00005004658	ENSMZEP00005009201	TAFH domain-containing protein.	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto.	0.902
LOC101467809	taf6	ENSMZEP00005004658	ENSMZEP00005021834	TAFH domain-containing protein.	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor.	0.953
LOC101469646	SRF	ENSMZEP00005000368	ENSMZEP00005013823	MADS-box domain-containing protein.	Serum response factor.	0.903
LOC101469646	nkx2-5	ENSMZEP00005000368	ENSMZEP00005011918	MADS-box domain-containing protein.	NK2 homeobox 5.	0.450
LOC101477738	LOC101467809	ENSMZEP00005001168	ENSMZEP00005004658	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	TAFH domain-containing protein.	0.636
LOC101477738	gtf2a1	ENSMZEP00005001168	ENSMZEP00005008243	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	General transcription factor IIA, 1.	0.782
LOC101477738	gtf2a2	ENSMZEP00005001168	ENSMZEP00005004377	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	Transcription initiation factor IIA subunit 2; TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation; Belongs to the TFIIA subunit 2 family.	0.840
LOC101477738	taf10	ENSMZEP00005001168	ENSMZEP00005027427	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	Transcription initiation factor TFIID subunit 10; TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors; Belongs to the TAF10 family.	0.929
LOC101477738	taf12	ENSMZEP00005001168	ENSMZEP00005005141	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor.	0.953
LOC101477738	taf13	ENSMZEP00005001168	ENSMZEP00005029636	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	TATA-box binding protein associated factor 13.	0.929
LOC101477738	taf3	ENSMZEP00005001168	ENSMZEP00005009201	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto.	0.902
LOC101477738	taf6	ENSMZEP00005001168	ENSMZEP00005021834	TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor.	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor.	0.953