(36 nodes) Positive regulation of DNA biosynthetic process network (Leptonychotes weddellii)

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:
	HGF	Hepatocyte growth factor; Potent mitogen for mature parenchymal hepatocyte cells, seems to be a hepatotrophic factor, and acts as a growth factor for a broad spectrum of tissues and cell types. Activating ligand for the receptor tyrosine kinase MET by binding to it and promoting its dimerization. Belongs to the peptidase S1 family. Plasminogen subfamily. (730 aa)
	PARN	poly(A)-specific ribonuclease PARN isoform X1. (638 aa)
	RFC3	Replication factor C subunit 3. (356 aa)
	POT1	Protection of telomeres protein 1-like. (516 aa)
	NEK7	Serine/threonine-protein kinase Nek7; Belongs to the protein kinase superfamily. (285 aa)
	GREM1	Gremlin. (184 aa)
	CCT2	T-complex protein 1 subunit beta. (543 aa)
	GINS3	DNA replication complex GINS protein PSF3 isoform X1. (216 aa)
	FGFR4	Fibroblast growth factor receptor. (800 aa)
	LOC102729936	T-complex protein 1 subunit alpha-like. (556 aa)
	LOC102746870	Chromosome transmission fidelity protein 8 homolog. (117 aa)
	MAP3K4	Mitogen-activated protein kinase kinase kinase 4 isoform X1. (1605 aa)
	PRKCQ	Protein kinase C; Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. PKC subfamily. (706 aa)
	LOC102740480	DNA replication complex GINS protein PSF2-like. (114 aa)
	PCNA	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. (261 aa)
	CCT3	T-complex protein 1 subunit gamma. (545 aa)
	FBXO4	F-box only protein 4. (387 aa)
	DKC1	H/ACA ribonucleoprotein complex subunit 4 isoform X1. (517 aa)
	HMBOX1	Homeobox-containing protein 1 isoform X1. (443 aa)
	POLG2	DNA polymerase subunit gamma-2, mitochondrial. (266 aa)
	WRAP53	Telomerase Cajal body protein 1. (532 aa)
	TNKS	Poly [ADP-ribose] polymerase. (1328 aa)
	RFC4	Replication factor C subunit 4. (363 aa)
	MAPK1	Mitogen-activated protein kinase; Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. MAP kinase subfamily. (326 aa)
	ATM	Serine-protein kinase ATM; Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]- Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and mo [...] (3054 aa)
	DSCC1	Sister chromatid cohesion protein DCC1. (392 aa)
	RFC2	Replication factor C subunit 2 isoform X1. (368 aa)
	LOC102737831	Serine/threonine-protein kinase D2-like. (246 aa)
	GINS4	DNA replication complex GINS protein SLD5. (162 aa)
	PDGFB	Platelet-derived growth factor subunit B isoform X1; Belongs to the PDGF/VEGF growth factor family. (241 aa)
	LOC102735621	Cyclin-dependent kinase 1-like. (387 aa)
	NEK2	Serine/threonine-protein kinase Nek2. (259 aa)
	LOC102747042	DNA polymerase subunit gamma-2, mitochondrial-like. (220 aa)
	LOC102730835	T-complex protein 1 subunit beta-like. (535 aa)
	FGF2	Fibroblast growth factor; Belongs to the heparin-binding growth factors family. (113 aa)
	ACD	LOW QUALITY PROTEIN: adrenocortical dysplasia homolog (Mouse). (494 aa)

Your Current Organism:

Leptonychotes weddellii

NCBI taxonomy Id: 9713
Other names: L. weddellii, Leptonychotes weddelli, Weddell seal

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
ACD	DKC1	A0A2U3ZA08	A0A2U3Y017	LOW QUALITY PROTEIN: adrenocortical dysplasia homolog (Mouse).	H/ACA ribonucleoprotein complex subunit 4 isoform X1.	0.552
ACD	POT1	A0A2U3ZA08	A0A2U3XCB6	LOW QUALITY PROTEIN: adrenocortical dysplasia homolog (Mouse).	Protection of telomeres protein 1-like.	0.999
ACD	WRAP53	A0A2U3ZA08	A0A2U3Y5L0	LOW QUALITY PROTEIN: adrenocortical dysplasia homolog (Mouse).	Telomerase Cajal body protein 1.	0.507
ATM	PCNA	A0A2U3YJR1	A0A2U3XVX8	Serine-protein kinase ATM; Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]- Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and mo [...]	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.	0.581
ATM	RFC2	A0A2U3YJR1	A0A2U3YR32	Serine-protein kinase ATM; Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]- Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and mo [...]	Replication factor C subunit 2 isoform X1.	0.735
ATM	RFC3	A0A2U3YJR1	A0A2U3XC21	Serine-protein kinase ATM; Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]- Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and mo [...]	Replication factor C subunit 3.	0.671
ATM	RFC4	A0A2U3YJR1	A0A2U3YHT9	Serine-protein kinase ATM; Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]- Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and mo [...]	Replication factor C subunit 4.	0.713
CCT2	CCT3	A0A2U3XLR2	A0A2U3XZ88	T-complex protein 1 subunit beta.	T-complex protein 1 subunit gamma.	0.999
CCT2	LOC102729936	A0A2U3XLR2	A0A2U3XQH4	T-complex protein 1 subunit beta.	T-complex protein 1 subunit alpha-like.	0.998
CCT3	CCT2	A0A2U3XZ88	A0A2U3XLR2	T-complex protein 1 subunit gamma.	T-complex protein 1 subunit beta.	0.999
CCT3	LOC102729936	A0A2U3XZ88	A0A2U3XQH4	T-complex protein 1 subunit gamma.	T-complex protein 1 subunit alpha-like.	0.999
CCT3	LOC102730835	A0A2U3XZ88	A0A2U3Z2Q0	T-complex protein 1 subunit gamma.	T-complex protein 1 subunit beta-like.	0.999
DKC1	ACD	A0A2U3Y017	A0A2U3ZA08	H/ACA ribonucleoprotein complex subunit 4 isoform X1.	LOW QUALITY PROTEIN: adrenocortical dysplasia homolog (Mouse).	0.552
DKC1	PARN	A0A2U3Y017	A0A2U3XBJ5	H/ACA ribonucleoprotein complex subunit 4 isoform X1.	poly(A)-specific ribonuclease PARN isoform X1.	0.493
DKC1	POT1	A0A2U3Y017	A0A2U3XCB6	H/ACA ribonucleoprotein complex subunit 4 isoform X1.	Protection of telomeres protein 1-like.	0.662
DKC1	WRAP53	A0A2U3Y017	A0A2U3Y5L0	H/ACA ribonucleoprotein complex subunit 4 isoform X1.	Telomerase Cajal body protein 1.	0.996
DSCC1	GINS3	A0A2U3YPN8	A0A2U3XNE5	Sister chromatid cohesion protein DCC1.	DNA replication complex GINS protein PSF3 isoform X1.	0.406
DSCC1	GINS4	A0A2U3YPN8	A0A2U3YSE2	Sister chromatid cohesion protein DCC1.	DNA replication complex GINS protein SLD5.	0.449
DSCC1	LOC102735621	A0A2U3YPN8	A0A2U3YVS6	Sister chromatid cohesion protein DCC1.	Cyclin-dependent kinase 1-like.	0.418
DSCC1	LOC102740480	A0A2U3YPN8	A0A2U3XU83	Sister chromatid cohesion protein DCC1.	DNA replication complex GINS protein PSF2-like.	0.799