(14 nodes) protein-DNA complex remodeling, and Transcription initiation from RNA polymerase II promoter network (Rhodnius prolixus)

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:
	R4FM47_RHOPR	Putative transcription factor tfb4. (297 aa)
	R4FM81_RHOPR	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity. (265 aa)
	R4FMM2_RHOPR	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. (113 aa)
	R4G2X9_RHOPR	Putative cdk activating kin; Belongs to the cyclin family. (329 aa)
	R4G445_RHOPR	Putative e3 ubiquitin ligase. (315 aa)
	R4G845_RHOPR	Putative transcription factor tfiih complex subunit tfb5. (71 aa)
	T1HG45_RHOPR	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. (450 aa)
	T1HP82_RHOPR	Uncharacterized protein. (581 aa)
	T1HPF2_RHOPR	Uncharacterized protein. (744 aa)
	T1HR08_RHOPR	TFIIB-type domain-containing protein. (250 aa)
	T1HWQ6_RHOPR	Transcription initiation factor IIE subunit beta; Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase. (259 aa)
	T1I4Q7_RHOPR	Helicase ATP-binding domain-containing protein. (756 aa)
	T1IC26_RHOPR	HTH TFE/IIEalpha-type domain-containing protein. (426 aa)
	T1IFS9_RHOPR	Uncharacterized protein. (127 aa)

Your Current Organism:

Rhodnius prolixus

NCBI taxonomy Id: 13249
Other names: R. prolixus

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
R4FM47_RHOPR	R4FM81_RHOPR	R4FM47	R4FM81	Putative transcription factor tfb4.	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	0.979
R4FM47_RHOPR	R4FMM2_RHOPR	R4FM47	R4FMM2	Putative transcription factor tfb4.	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.	0.984
R4FM47_RHOPR	R4G2X9_RHOPR	R4FM47	R4G2X9	Putative transcription factor tfb4.	Putative cdk activating kin; Belongs to the cyclin family.	0.998
R4FM47_RHOPR	R4G445_RHOPR	R4FM47	R4G445	Putative transcription factor tfb4.	Putative e3 ubiquitin ligase.	0.998
R4FM47_RHOPR	R4G845_RHOPR	R4FM47	R4G845	Putative transcription factor tfb4.	Putative transcription factor tfiih complex subunit tfb5.	0.996
R4FM47_RHOPR	T1HG45_RHOPR	R4FM47	T1HG45	Putative transcription factor tfb4.	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.	0.999
R4FM47_RHOPR	T1HP82_RHOPR	R4FM47	T1HP82	Putative transcription factor tfb4.	Uncharacterized protein.	0.999
R4FM47_RHOPR	T1HPF2_RHOPR	R4FM47	T1HPF2	Putative transcription factor tfb4.	Uncharacterized protein.	0.998
R4FM47_RHOPR	T1HR08_RHOPR	R4FM47	T1HR08	Putative transcription factor tfb4.	TFIIB-type domain-containing protein.	0.985
R4FM47_RHOPR	T1HWQ6_RHOPR	R4FM47	T1HWQ6	Putative transcription factor tfb4.	Transcription initiation factor IIE subunit beta; Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.	0.995
R4FM47_RHOPR	T1I4Q7_RHOPR	R4FM47	T1I4Q7	Putative transcription factor tfb4.	Helicase ATP-binding domain-containing protein.	0.998
R4FM47_RHOPR	T1IC26_RHOPR	R4FM47	T1IC26	Putative transcription factor tfb4.	HTH TFE/IIEalpha-type domain-containing protein.	0.995
R4FM47_RHOPR	T1IFS9_RHOPR	R4FM47	T1IFS9	Putative transcription factor tfb4.	Uncharacterized protein.	0.972
R4FM81_RHOPR	R4FM47_RHOPR	R4FM81	R4FM47	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	Putative transcription factor tfb4.	0.979
R4FM81_RHOPR	R4FMM2_RHOPR	R4FM81	R4FMM2	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	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.	0.983
R4FM81_RHOPR	R4G2X9_RHOPR	R4FM81	R4G2X9	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	Putative cdk activating kin; Belongs to the cyclin family.	0.967
R4FM81_RHOPR	R4G445_RHOPR	R4FM81	R4G445	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	Putative e3 ubiquitin ligase.	0.986
R4FM81_RHOPR	R4G845_RHOPR	R4FM81	R4G845	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	Putative transcription factor tfiih complex subunit tfb5.	0.901
R4FM81_RHOPR	T1HG45_RHOPR	R4FM81	T1HG45	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	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.	0.986
R4FM81_RHOPR	T1HP82_RHOPR	R4FM81	T1HP82	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.	Uncharacterized protein.	0.978