(54 nodes) RNA Polymerase I Transcription network (Pygoscelis adeliae)

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:
	RRN3	RNA polymerase I-specific transcription initiation factor RRN3. (616 aa)
	POLR1A	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1671 aa)
	TWISTNB	DNA-directed RNA polymerase I subunit RPA43. (249 aa)
	CCNH	Cyclin-H; Belongs to the cyclin family. (265 aa)
	AS28_14622	Histone H2A; Belongs to the histone H2A family. (104 aa)
	AS28_11934	Uncharacterized protein. (234 aa)
	POLR1B	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1020 aa)
	MNAT1	CDK-activating kinase assembly factor MAT1. (279 aa)
	AS28_08341	Histone H2B; Belongs to the histone H2B family. (98 aa)
	POLR2E	DNA-directed RNA polymerases I, II, and III subunit RPABC1. (132 aa)
	RBBP4	Histone-binding protein RBBP4. (420 aa)
	TAF1B	TATA box-binding protein-associated factor RNA polymerase I subunit B. (572 aa)
	AS28_12563	Histone H2B; Belongs to the histone H2B family. (126 aa)
	AS28_12570	Histone H3. (96 aa)
	GTF2H5	General transcription factor IIH subunit 5. (59 aa)
	GTF2H3	General transcription factor IIH subunit 3. (305 aa)
	TBP	TATA-box-binding protein. (299 aa)
	AS28_05161	DNA-directed RNA polymerases I and III subunit RPAC1. (266 aa)
	ACRC	Acidic repeat-containing protein. (232 aa)
	AS28_12562	Histone H2B; Belongs to the histone H2B family. (126 aa)
	AS28_12574	Histone H2B; Belongs to the histone H2B family. (126 aa)
	CHD4	Chromodomain-helicase-DNA-binding protein 4. (1928 aa)
	AS28_12560	Histone H2B; Belongs to the histone H2B family. (126 aa)
	AS28_12572	Histone H2A; Belongs to the histone H2A family. (129 aa)
	AS28_12578	Histone H2A; Belongs to the histone H2A family. (89 aa)
	TAF1A	TATA box-binding protein-associated factor RNA polymerase I subunit A. (412 aa)
	ERCC6	DNA excision repair protein ERCC-6. (1507 aa)
	AS28_12564	Histone H2B; Belongs to the histone H2B family. (126 aa)
	AS28_12566	Histone H2B; Belongs to the histone H2B family. (126 aa)
	TBPL1	TATA box-binding protein-like 1. (161 aa)
	AS28_02578	TATA box-binding protein-associated factor RNA polymerase I subunit D. (197 aa)
	AS28_12561	Histone H3; Belongs to the histone H3 family. (133 aa)
	AS28_12568	Histone H4; Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. (103 aa)
	AS28_12573	Histone H3. (121 aa)
	DMTF1	Cyclin-D-binding Myb-like transcription factor 1. (752 aa)
	MBD2	Methyl-CpG-binding domain protein 2. (190 aa)
	TTF1	Transcription termination factor 1. (349 aa)
	TBPL2	TATA-box-binding protein. (170 aa)
	POLR2H	DNA-directed RNA polymerases I, II, and III subunit RPABC3. (126 aa)
	ERCC3	TFIIH basal transcription factor complex helicase XPB subunit. (705 aa)
	CBX3	Chromobox protein 3. (176 aa)
	RBBP7	Histone-binding protein RBBP7. (419 aa)
	AS28_06757	Myomodulin neuropeptides 1. (107 aa)
	CDK7	Cyclin-dependent kinase 7. (316 aa)
	PTRF	Polymerase I and transcript release factor. (361 aa)
	AS28_07752	Histone H2B; Belongs to the histone H2B family. (126 aa)
	H3F3B	Histone H3; Belongs to the histone H3 family. (136 aa)
	MTA3	Metastasis-associated protein MTA3. (586 aa)
	GTF2H1	General transcription factor IIH subunit 1. (548 aa)
	GTF2H2	General transcription factor IIH subunit 2. (401 aa)
	AS28_03911	DNA-directed RNA polymerases I, II, and III subunit RPABC4. (55 aa)
	AS28_11685	Chromodomain-helicase-DNA-binding protein 5. (1808 aa)
	MBD3	Methyl-CpG-binding domain protein 3. (253 aa)
	AS28_11535	DNA-directed RNA polymerases I, II, and III subunit RPABC5. (67 aa)

Your Current Organism:

Pygoscelis adeliae

NCBI taxonomy Id: 9238
Other names: Adelie penguin, P. adeliae, Pygoscelis adelia

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
ACRC	AS28_02578	A0A093RNP2	A0A093NLL9	Acidic repeat-containing protein.	TATA box-binding protein-associated factor RNA polymerase I subunit D.	0.736
ACRC	AS28_06757	A0A093RNP2	A0A093NXR7	Acidic repeat-containing protein.	Myomodulin neuropeptides 1.	0.512
ACRC	POLR1A	A0A093RNP2	A0A093P6U8	Acidic repeat-containing protein.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.516
ACRC	POLR1B	A0A093RNP2	A0A093PDK3	Acidic repeat-containing protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.480
ACRC	POLR2H	A0A093RNP2	A0A093NQX5	Acidic repeat-containing protein.	DNA-directed RNA polymerases I, II, and III subunit RPABC3.	0.403
ACRC	RRN3	A0A093RNP2	A0A093P5T6	Acidic repeat-containing protein.	RNA polymerase I-specific transcription initiation factor RRN3.	0.561
ACRC	TAF1B	A0A093RNP2	A0A093PLP1	Acidic repeat-containing protein.	TATA box-binding protein-associated factor RNA polymerase I subunit B.	0.763
ACRC	TBP	A0A093RNP2	A0A093RIM3	Acidic repeat-containing protein.	TATA-box-binding protein.	0.512
ACRC	TBPL1	A0A093RNP2	A0A093NHQ6	Acidic repeat-containing protein.	TATA box-binding protein-like 1.	0.512
ACRC	TBPL2	A0A093RNP2	A0A093NQ93	Acidic repeat-containing protein.	TATA-box-binding protein.	0.512
AS28_02578	ACRC	A0A093NLL9	A0A093RNP2	TATA box-binding protein-associated factor RNA polymerase I subunit D.	Acidic repeat-containing protein.	0.736
AS28_02578	AS28_05161	A0A093NLL9	A0A093RMG0	TATA box-binding protein-associated factor RNA polymerase I subunit D.	DNA-directed RNA polymerases I and III subunit RPAC1.	0.508
AS28_02578	AS28_06757	A0A093NLL9	A0A093NXR7	TATA box-binding protein-associated factor RNA polymerase I subunit D.	Myomodulin neuropeptides 1.	0.640
AS28_02578	AS28_14622	A0A093NLL9	A0A093PAE5	TATA box-binding protein-associated factor RNA polymerase I subunit D.	Histone H2A; Belongs to the histone H2A family.	0.462
AS28_02578	DMTF1	A0A093NLL9	A0A093NN69	TATA box-binding protein-associated factor RNA polymerase I subunit D.	Cyclin-D-binding Myb-like transcription factor 1.	0.486
AS28_02578	GTF2H5	A0A093NLL9	A0A093QYB0	TATA box-binding protein-associated factor RNA polymerase I subunit D.	General transcription factor IIH subunit 5.	0.515
AS28_02578	POLR1A	A0A093NLL9	A0A093P6U8	TATA box-binding protein-associated factor RNA polymerase I subunit D.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.542
AS28_02578	POLR1B	A0A093NLL9	A0A093PDK3	TATA box-binding protein-associated factor RNA polymerase I subunit D.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.556
AS28_02578	POLR2E	A0A093NLL9	A0A093PJ40	TATA box-binding protein-associated factor RNA polymerase I subunit D.	DNA-directed RNA polymerases I, II, and III subunit RPABC1.	0.522
AS28_02578	RRN3	A0A093NLL9	A0A093P5T6	TATA box-binding protein-associated factor RNA polymerase I subunit D.	RNA polymerase I-specific transcription initiation factor RRN3.	0.564