(94 nodes) Positive regulation of DNA repair network (Cyprinodon variegatus)

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:
	LOC107102680	Eyes absent homolog; Belongs to the HAD-like hydrolase superfamily. EYA family. (596 aa)
	LOC107082085	RING-type domain-containing protein. (263 aa)
	mcrs1	Microspherule protein 1. (430 aa)
	timeless	Timeless circadian clock. (1251 aa)
	mms19	MMS19 homolog, cytosolic iron-sulfur assembly component. (846 aa)
	hdgfl2	HDGF like 2. (657 aa)
	ENSCVAP00000001305	Pogo transposable element derived with ZNF domain a. (1226 aa)
	ino80d	INO80 complex subunit Da. (994 aa)
	LOC107095754	Actin-related protein 2; ATP-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF). The Arp2/3 complex mediates the formation of branched actin networks in the cytoplasm, providing the force for cell motility. Seems to contact the pointed end of the daughter actin filament. (399 aa)
	babam2	BRISC and BRCA1 A complex member 2. (386 aa)
	ercc6	Excision repair cross-complementation group 6. (1441 aa)
	spire2	Spire-type actin nucleation factor 2. (771 aa)
	shld2	Si:ch211-134m17.9. (772 aa)
	prkdc	Protein kinase, DNA-activated, catalytic subunit; Belongs to the PI3/PI4-kinase family. (3872 aa)
	ENSCVAP00000003552	Uncharacterized protein. (74 aa)
	ENSCVAP00000003657	Uncharacterized protein. (373 aa)
	LOC107095150	RING-type domain-containing protein. (198 aa)
	LOC107095145	Zgc:66440. (369 aa)
	sirt6	Sirtuin 6. (349 aa)
	sirt1	Sirtuin 1. (691 aa)
	bcl7a	BAF chromatin remodeling complex subunit BCL7A. (228 aa)
	slf1	SMC5-SMC6 complex localization factor 1. (877 aa)
	ENSCVAP00000005508	HTH_Tnp_Tc3_2 domain-containing protein. (133 aa)
	fam168a	Family with sequence similarity 168 member A. (226 aa)
	tmem161a	Transmembrane protein 161A. (493 aa)
	ENSCVAP00000006814	DDE_3 domain-containing protein. (87 aa)
	ENSCVAP00000006883	DDE_3 domain-containing protein. (156 aa)
	LOC107085383	Structural maintenance of chromosomes flexible hinge domain containing 1. (1708 aa)
	LOC107097796	Uncharacterized protein. (250 aa)
	ENSCVAP00000007791	RING-type domain-containing protein. (203 aa)
	ENSCVAP00000008191	Reverse transcriptase domain-containing protein. (509 aa)
	ccdc117	Si:ch211-102c2.7. (250 aa)
	ercc8	Excision repair cross-complementation group 8. (401 aa)
	ENSCVAP00000009952	Uncharacterized protein. (222 aa)
	ENSCVAP00000009967	Uncharacterized protein. (586 aa)
	LOC107081848	Enhancer of polycomb homolog. (848 aa)
	LOC107085266	Zgc:101810; Belongs to the actin family. (394 aa)
	nfrkb	Nuclear factor related to kappaB binding protein. (1278 aa)
	LOC107085781	TP53 induced glycolysis regulatory phosphatase b. (239 aa)
	wdr48	WD repeat domain 48b. (698 aa)
	LOC107083102	Uncharacterized protein. (446 aa)
	fancb	FA complementation group B. (726 aa)
	ENSCVAP00000013653	DDE_3 domain-containing protein. (97 aa)
	pnkp	Polynucleotide kinase 3'-phosphatase. (600 aa)
	LOC107096940	SET domain-containing protein. (1939 aa)
	rnf168	E3 ubiquitin-protein ligase RNF168; E3 ubiquitin-protein ligase required for accumulation of repair proteins to sites of DNA damage. Acts with UBE2N/UBC13 to amplify the RNF8-dependent histone ubiquitination. Recruited to sites of DNA damage at double-strand breaks (DSBs) by binding to ubiquitinated histone H2A and ubiquitinates histone H2A and H2AX, leading to amplify the RNF8-dependent H2A ubiquitination and promoting the formation of 'Lys-63'-linked ubiquitin conjugates. This leads to concentrate ubiquitinated histones H2A and H2AX at DNA lesions to the threshold required for recrui [...] (426 aa)
	uchl5	Ubiquitin carboxyl-terminal hydrolase. (329 aa)
	wrap53	WD repeat containing, antisense to TP53. (507 aa)
	foxm1	Forkhead box M1. (649 aa)
	arid2	AT rich interactive domain 2 (ARID, RFX-like). (1628 aa)
	pias4	Protein inhibitor of activated STAT, 4a. (508 aa)
	ENSCVAP00000016264	Uncharacterized protein. (202 aa)
	helq	Helicase, POLQ like. (897 aa)
	mgmt	O-6-methylguanine-DNA methyltransferase. (188 aa)
	LOC107084223	HTH_Tnp_Tc3_2 domain-containing protein. (180 aa)
	dmap1	DNA methyltransferase 1 associated protein 1. (487 aa)
	LOC107092483	Spire-type actin nucleation factor 1a. (778 aa)
	LOC107092437	Si:dkey-3h3.3. (339 aa)
	trrap	Transformation/transcription domain-associated protein; Belongs to the PI3/PI4-kinase family. (2570 aa)
	ENSCVAP00000018429	Uncharacterized protein. (267 aa)
	babam1	BRISC and BRCA1 A complex member 1. (380 aa)
	ino80e	INO80 complex subunit E. (247 aa)
	ENSCVAP00000019965	WGR domain-containing protein. (153 aa)
	parp3	Poly [ADP-ribose] polymerase. (525 aa)
	ENSCVAP00000020299	RING-type domain-containing protein. (196 aa)
	rnf8	E3 ubiquitin-protein ligase RNF8; E3 ubiquitin-protein ligase that plays a key role in DNA damage signaling via 2 distinct roles: by mediating the 'Lys-63'-linked ubiquitination of histones H2A and H2AX and promoting the recruitment of DNA repair proteins at double-strand breaks (DSBs) sites, and by catalyzing 'Lys-48'-linked ubiquitination to remove target proteins from DNA damage sites. Following DNA DSBs, it is recruited to the sites of damage by ATM-phosphorylated MDC1 and catalyzes the 'Lys-63'-linked ubiquitination of histones H2A and H2AX, thereby promoting the formation of TP53 [...] (514 aa)
	ENSCVAP00000022195	DDE_3 domain-containing protein. (120 aa)
	mrgbp	MRG/MORF4L binding protein. (192 aa)
	vps72	Vacuolar protein sorting 72 homolog a. (368 aa)
	actl6a	Actin-like 6A; Belongs to the actin family. (429 aa)
	tfpt	Uncharacterized protein. (198 aa)
	ENSCVAP00000024720	SMC hinge domain-containing protein. (1613 aa)
	dhx9	DEAH (Asp-Glu-Ala-His) box helicase 9. (1216 aa)
	LOC107084302	TP53 induced glycolysis regulatory phosphatase a. (266 aa)
	ENSCVAP00000026869	Pogo transposable element derived with ZNF domain b. (1875 aa)
	LOC107090369	Enhancer of polycomb homolog. (831 aa)
	LOC107090597	Uncharacterized protein. (1276 aa)
	ENSCVAP00000027436	Uncharacterized protein. (331 aa)
	mfsd11	Major facilitator superfamily domain containing 11. (454 aa)
	uimc1	Uncharacterized protein. (990 aa)
	yeats4	YEATS domain containing 4. (226 aa)
	xrcc1	X-ray repair complementing defective repair in Chinese hamster cells 1. (623 aa)
	LOC107080723	RING-type domain-containing protein. (210 aa)
	ENSCVAP00000028757	RING-type domain-containing protein. (536 aa)
	ENSCVAP00000029582	SMC hinge domain-containing protein. (570 aa)
	ENSCVAP00000030549	Uncharacterized protein. (79 aa)
	LOC107082340	SET domain and mariner transposase fusion gene. (283 aa)
	abraxas1	Abraxas 1, BRCA1 A complex subunit. (317 aa)
	parp1	Poly [ADP-ribose] polymerase; Poly-ADP-ribosyltransferase that mediates poly-ADP- ribosylation of proteins and plays a key role in DNA repair. (979 aa)
	brca1	Uncharacterized protein. (1314 aa)
	ino80	INO80 complex ATPase subunit. (1564 aa)
	spire1	KIND domain-containing protein. (620 aa)
	rif1	Replication timing regulatory factor 1. (2380 aa)
	kmt5b	Lysine methyltransferase 5B. (855 aa)

Your Current Organism:

Cyprinodon variegatus

NCBI taxonomy Id: 28743
Other names: C. variegatus, sheepshead minnow

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
ENSCVAP00000008191	abraxas1	ENSCVAP00000008191	ENSCVAP00000031199	Reverse transcriptase domain-containing protein.	Abraxas 1, BRCA1 A complex subunit.	0.430
ENSCVAP00000008191	babam1	ENSCVAP00000008191	ENSCVAP00000018674	Reverse transcriptase domain-containing protein.	BRISC and BRCA1 A complex member 1.	0.974
ENSCVAP00000008191	babam2	ENSCVAP00000008191	ENSCVAP00000002402	Reverse transcriptase domain-containing protein.	BRISC and BRCA1 A complex member 2.	0.974
ENSCVAP00000008191	brca1	ENSCVAP00000008191	ENSCVAP00000031835	Reverse transcriptase domain-containing protein.	Uncharacterized protein.	0.963
ENSCVAP00000008191	pias4	ENSCVAP00000008191	ENSCVAP00000014848	Reverse transcriptase domain-containing protein.	Protein inhibitor of activated STAT, 4a.	0.608
ENSCVAP00000008191	rif1	ENSCVAP00000008191	ENSCVAP00000032456	Reverse transcriptase domain-containing protein.	Replication timing regulatory factor 1.	0.510
ENSCVAP00000008191	rnf168	ENSCVAP00000008191	ENSCVAP00000013993	Reverse transcriptase domain-containing protein.	E3 ubiquitin-protein ligase RNF168; E3 ubiquitin-protein ligase required for accumulation of repair proteins to sites of DNA damage. Acts with UBE2N/UBC13 to amplify the RNF8-dependent histone ubiquitination. Recruited to sites of DNA damage at double-strand breaks (DSBs) by binding to ubiquitinated histone H2A and ubiquitinates histone H2A and H2AX, leading to amplify the RNF8-dependent H2A ubiquitination and promoting the formation of 'Lys-63'-linked ubiquitin conjugates. This leads to concentrate ubiquitinated histones H2A and H2AX at DNA lesions to the threshold required for recrui [...]	0.696
ENSCVAP00000008191	rnf8	ENSCVAP00000008191	ENSCVAP00000021481	Reverse transcriptase domain-containing protein.	E3 ubiquitin-protein ligase RNF8; E3 ubiquitin-protein ligase that plays a key role in DNA damage signaling via 2 distinct roles: by mediating the 'Lys-63'-linked ubiquitination of histones H2A and H2AX and promoting the recruitment of DNA repair proteins at double-strand breaks (DSBs) sites, and by catalyzing 'Lys-48'-linked ubiquitination to remove target proteins from DNA damage sites. Following DNA DSBs, it is recruited to the sites of damage by ATM-phosphorylated MDC1 and catalyzes the 'Lys-63'-linked ubiquitination of histones H2A and H2AX, thereby promoting the formation of TP53 [...]	0.723
ENSCVAP00000009952	LOC107084302	ENSCVAP00000009952	ENSCVAP00000025625	Uncharacterized protein.	TP53 induced glycolysis regulatory phosphatase a.	0.905
ENSCVAP00000009952	LOC107085781	ENSCVAP00000009952	ENSCVAP00000012680	Uncharacterized protein.	TP53 induced glycolysis regulatory phosphatase b.	0.901
ENSCVAP00000009967	ENSCVAP00000018429	ENSCVAP00000009967	ENSCVAP00000018429	Uncharacterized protein.	Uncharacterized protein.	0.567
ENSCVAP00000009967	LOC107081848	ENSCVAP00000009967	ENSCVAP00000010288	Uncharacterized protein.	Enhancer of polycomb homolog.	0.514
ENSCVAP00000009967	LOC107090369	ENSCVAP00000009967	ENSCVAP00000027287	Uncharacterized protein.	Enhancer of polycomb homolog.	0.514
ENSCVAP00000009967	actl6a	ENSCVAP00000009967	ENSCVAP00000023955	Uncharacterized protein.	Actin-like 6A; Belongs to the actin family.	0.844
ENSCVAP00000009967	dmap1	ENSCVAP00000009967	ENSCVAP00000017657	Uncharacterized protein.	DNA methyltransferase 1 associated protein 1.	0.676
ENSCVAP00000009967	ercc8	ENSCVAP00000009967	ENSCVAP00000009414	Uncharacterized protein.	Excision repair cross-complementation group 8.	0.426
ENSCVAP00000009967	ino80d	ENSCVAP00000009967	ENSCVAP00000001684	Uncharacterized protein.	INO80 complex subunit Da.	0.824
ENSCVAP00000009967	ino80e	ENSCVAP00000009967	ENSCVAP00000019100	Uncharacterized protein.	INO80 complex subunit E.	0.947
ENSCVAP00000009967	mcrs1	ENSCVAP00000009967	ENSCVAP00000000832	Uncharacterized protein.	Microspherule protein 1.	0.823
ENSCVAP00000009967	mrgbp	ENSCVAP00000009967	ENSCVAP00000022665	Uncharacterized protein.	MRG/MORF4L binding protein.	0.548