(66 nodes) Nucleotide excision repair network (Caenorhabditis remanei)

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:
	CRE_17775	Uncharacterized protein. (679 aa)
	Cre-rad-23	CRE-RAD-23 protein. (323 aa)
	CRE_02255	ERCC4 domain-containing protein. (383 aa)
	CRE_02256	Uncharacterized protein. (640 aa)
	CRE_27041	DNA polymerase. (1080 aa)
	CRE_27397	Uncharacterized protein. (385 aa)
	Cre-cul-4	CRE-CUL-4 protein; Belongs to the cullin family. (841 aa)
	Cre-cyn-10	Peptidyl-prolyl cis-trans isomerase; PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides; Belongs to the cyclophilin-type PPIase family. (162 aa)
	CRE_26065	CBFD_NFYB_HMF domain-containing protein. (212 aa)
	CRE_26066	CBFD_NFYB_HMF domain-containing protein. (212 aa)
	CRE_26091	Uncharacterized protein. (1175 aa)
	Cre-rpa-1	Replication protein A subunit; As part of the heterotrimeric replication protein A complex (RPA/RP-A), binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism. Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage. (656 aa)
	CRE_25211	Uncharacterized protein. (317 aa)
	CRE_25217	General transcription factor IIH subunit. (376 aa)
	CRE_25372	Uncharacterized protein. (194 aa)
	CRE_25102	Uncharacterized protein. (325 aa)
	Cre-rpa-4	CRE-RPA-4 protein. (292 aa)
	CRE_03137	Uncharacterized protein. (447 aa)
	CRE_03180	CBFD_NFYB_HMF domain-containing protein. (150 aa)
	CRE_04799	Helicase ATP-binding domain-containing protein. (850 aa)
	Cre-cyh-1	CRE-CYH-1 protein. (330 aa)
	CRE_08225	Uncharacterized protein. (247 aa)
	Cre-cdk-7	CRE-CDK-7 protein; Belongs to the protein kinase superfamily. (329 aa)
	CRE_08005	Uncharacterized protein. (880 aa)
	Cre-rfc-3	CRE-RFC-3 protein. (370 aa)
	CRE_10300	SAP domain-containing protein. (430 aa)
	CRE_10057	Uncharacterized protein. (531 aa)
	CRE_12625	Uncharacterized protein. (452 aa)
	CRE_13961	DNA polymerase epsilon catalytic subunit; DNA polymerase II participates in chromosomal DNA replication; Belongs to the DNA polymerase type-B family. (2200 aa)
	Cre-csb-1	CRE-CSB-1 protein. (918 aa)
	Cre-rfc-4	CRE-RFC-4 protein. (362 aa)
	CRE_20701	Uncharacterized protein. (751 aa)
	Cre-rfc-2	CRE-RFC-2 protein. (329 aa)
	Cre-rbx-1	CRE-RBX-1 protein. (112 aa)
	CRE_01011	Uncharacterized protein. (797 aa)
	CRE_27629	Protein kinase domain-containing protein; Belongs to the protein kinase superfamily. (318 aa)
	CRE_25692	Uncharacterized protein. (72 aa)
	Cre-rfc-1	Replication factor C subunit 1. (835 aa)
	CRE_06764	AAA domain-containing protein. (365 aa)
	Cre-mdt-30	CRE-MDT-30 protein. (537 aa)
	CRE_16215	Helicase ATP-binding domain-containing protein. (789 aa)
	CRE_15525	Protein kinase domain-containing protein. (325 aa)
	Cre-ddb-1	CRE-DDB-1 protein. (1154 aa)
	Cre-xpg-1	CRE-XPG-1 protein. (828 aa)
	Cre-mnat-1	CDK-activating kinase assembly factor MAT1; Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. (313 aa)
	Cre-lin-9	CRE-LIN-9 protein. (647 aa)
	Cre-pcn-1	Proliferating cell nuclear antigen; This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand; Belongs to the PCNA family. (229 aa)
	Cre-pole-2	DNA polymerase epsilon subunit; Participates in DNA repair and in chromosomal DNA replication; Belongs to the DNA polymerase epsilon subunit B family. (520 aa)
	CRE_18098	Uncharacterized protein. (56 aa)
	Cre-lig-1	DNA ligase. (779 aa)
	Cre-rpa-2	CRE-RPA-2 protein. (289 aa)
	CRE_19970	Uncharacterized protein. (1097 aa)
	CRE_01317	PH_TFIIH domain-containing protein. (436 aa)
	CRE_03403	PCNA_N domain-containing protein. (219 aa)
	CRE_20976	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. (128 aa)
	CRE_20979	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. (470 aa)
	Cre-xpc-1	CRE-XPC-1 protein. (1101 aa)
	CRE_30262	Uncharacterized protein. (101 aa)
	CRE_21072	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. (468 aa)
	CRE_19592	Protein kinase domain-containing protein. (167 aa)
	CRE_26014	Uncharacterized protein. (255 aa)
	CRE_02776	BRCT domain-containing protein. (1202 aa)
	CRE_07177	Uncharacterized protein. (236 aa)
	CRE_04493	AAA domain-containing protein. (252 aa)
	CRE_17719	Uncharacterized protein. (261 aa)
	CRE_30357	Uncharacterized protein. (440 aa)

Your Current Organism:

Caenorhabditis remanei

NCBI taxonomy Id: 31234
Other names: C. remanei, Caenorhabditis vulgaris

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
CRE_01011	CRE_01317	E3MID2	E3N9N3	Uncharacterized protein.	PH_TFIIH domain-containing protein.	0.987
CRE_01011	CRE_02255	E3MID2	E3LFX0	Uncharacterized protein.	ERCC4 domain-containing protein.	0.879
CRE_01011	CRE_02256	E3MID2	E3LFX2	Uncharacterized protein.	Uncharacterized protein.	0.901
CRE_01011	CRE_03137	E3MID2	E3LWS2	Uncharacterized protein.	Uncharacterized protein.	0.980
CRE_01011	CRE_03180	E3MID2	E3LWZ7	Uncharacterized protein.	CBFD_NFYB_HMF domain-containing protein.	0.676
CRE_01011	CRE_03403	E3MID2	E3NAL8	Uncharacterized protein.	PCNA_N domain-containing protein.	0.689
CRE_01011	CRE_04493	E3MID2	E3NWI1	Uncharacterized protein.	AAA domain-containing protein.	0.706
CRE_01011	CRE_04799	E3MID2	E3LZB1	Uncharacterized protein.	Helicase ATP-binding domain-containing protein.	0.975
CRE_01011	CRE_06764	E3MID2	E3MP05	Uncharacterized protein.	AAA domain-containing protein.	0.717
CRE_01011	CRE_07177	E3MID2	E3NU33	Uncharacterized protein.	Uncharacterized protein.	0.776
CRE_01011	CRE_08005	E3MID2	E3M3R6	Uncharacterized protein.	Uncharacterized protein.	0.862
CRE_01011	CRE_08225	E3MID2	E3M355	Uncharacterized protein.	Uncharacterized protein.	0.849
CRE_01011	CRE_10057	E3MID2	E3M705	Uncharacterized protein.	Uncharacterized protein.	0.996
CRE_01011	CRE_10300	E3MID2	E3M6D6	Uncharacterized protein.	SAP domain-containing protein.	0.717
CRE_01011	CRE_13961	E3MID2	E3M8Z6	Uncharacterized protein.	DNA polymerase epsilon catalytic subunit; DNA polymerase II participates in chromosomal DNA replication; Belongs to the DNA polymerase type-B family.	0.735
CRE_01011	CRE_15525	E3MID2	E3MSR2	Uncharacterized protein.	Protein kinase domain-containing protein.	0.962
CRE_01011	CRE_16215	E3MID2	E3MSM2	Uncharacterized protein.	Helicase ATP-binding domain-containing protein.	0.999
CRE_01011	CRE_17775	E3MID2	E3NU81	Uncharacterized protein.	Uncharacterized protein.	0.618
CRE_01011	CRE_18098	E3MID2	E3N327	Uncharacterized protein.	Uncharacterized protein.	0.776
CRE_01011	CRE_19592	E3MID2	E3NRY3	Uncharacterized protein.	Protein kinase domain-containing protein.	0.962