(77 nodes) Positive regulation of gene expression network (Vitis vinifera)

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:
	F6GV38_VITVI	RRM domain-containing protein. (106 aa)
	VITISV_032904	PHD domain-containing protein. (683 aa)
	VITISV_032681	Epimerase domain-containing protein. (378 aa)
	VITISV_010162	Tr-type G domain-containing protein. (464 aa)
	VITISV_017448	RPOL4c domain-containing protein. (138 aa)
	VITISV_039540	Epimerase domain-containing protein. (397 aa)
	VITISV_009952	Uncharacterized protein. (172 aa)
	VITISV_018888	Eukaryotic translation initiation factor 5A. (159 aa)
	VITISV_043015	Mago-bind domain-containing protein. (234 aa)
	VITISV_014697	Eukaryotic translation initiation factor 5A. (160 aa)
	VITISV_042914	Uncharacterized protein. (176 aa)
	VITISV_020593	Eukaryotic translation initiation factor 5A. (160 aa)
	D7FBA7_VITVI	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family. (197 aa)
	D7SHM6_VITVI	JmjC domain-containing protein. (498 aa)
	D7SP05_VITVI	Uncharacterized protein. (325 aa)
	D7SQD3_VITVI	Uncharacterized protein. (821 aa)
	D7SR91_VITVI	NAC domain-containing protein. (313 aa)
	D7SW49_VITVI	Uncharacterized protein. (333 aa)
	D7SWK1_VITVI	Translation factor GUF1 homolog, chloroplastic; Promotes chloroplast protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. (680 aa)
	D7T1S3_VITVI	RRM domain-containing protein. (260 aa)
	D7TD48_VITVI	Uncharacterized protein. (740 aa)
	D7TGS2_VITVI	Smg4_UPF3 domain-containing protein. (519 aa)
	D7TI58_VITVI	Uncharacterized protein. (306 aa)
	D7TNB0_VITVI	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family. (197 aa)
	D7TND8_VITVI	Uncharacterized protein. (377 aa)
	D7TUX0_VITVI	Ribosomal_S4 domain-containing protein. (132 aa)
	D7U780_VITVI	Uncharacterized protein. (89 aa)
	D7U9M6_VITVI	Eukaryotic translation initiation factor 3 subunit H; Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. (337 aa)
	D7UBU1_VITVI	Tr-type G domain-containing protein. (464 aa)
	D7UD36_VITVI	Uncharacterized protein. (36 aa)
	F6GSX9_VITVI	Non-specific serine/threonine protein kinase; Belongs to the protein kinase superfamily. (452 aa)
	F6GT09_VITVI	DUF4210 domain-containing protein. (765 aa)
	F6GTM2_VITVI	Uncharacterized protein. (1246 aa)
	F6GUU8_VITVI	RRM domain-containing protein. (287 aa)
	F6I6P7_VITVI	DSHCT domain-containing protein. (63 aa)
	F6GVX3_VITVI	NAC domain-containing protein. (359 aa)
	F6GWG5_VITVI	HTH myb-type domain-containing protein. (304 aa)
	F6GWY0_VITVI	Uncharacterized protein. (373 aa)
	F6GX65_VITVI	PPR_long domain-containing protein. (763 aa)
	F6GXW1_VITVI	Uncharacterized protein; Belongs to the protein kinase superfamily. (489 aa)
	F6GYB4_VITVI	Smg4_UPF3 domain-containing protein. (341 aa)
	F6GYB6_VITVI	Smg4_UPF3 domain-containing protein. (357 aa)
	F6GYP1_VITVI	Uncharacterized protein. (76 aa)
	F6GYP2_VITVI	Uncharacterized protein. (202 aa)
	rps4	30S ribosomal protein S4, chloroplastic; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. Belongs to the universal ribosomal protein uS4 family. (201 aa)
	F6GYV6_VITVI	Uncharacterized protein. (757 aa)
	F6H077_VITVI	5'-3' exoribonuclease; Possesses 5'->3' exoribonuclease activity. Acts as an endogenous post-transcriptional gene silencing (PTGS) suppressor. (1065 aa)
	F6H2L9_VITVI	eIF-5a domain-containing protein. (114 aa)
	F6H451_VITVI	DUF4210 domain-containing protein. (669 aa)
	F6H5P1_VITVI	Translation factor GUF1 homolog, mitochondrial; Promotes mitochondrial protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Binds to mitochondrial ribosomes in a GTP-dependent manner. (681 aa)
	F6H676_VITVI	Uncharacterized protein. (811 aa)
	F6H7C0_VITVI	TMF_TATA_bd domain-containing protein. (978 aa)
	F6H9P7_VITVI	Uncharacterized protein. (995 aa)
	F6HCW3_VITVI	Smr domain-containing protein. (701 aa)
	F6HCW7_VITVI	Uncharacterized protein. (221 aa)
	F6HFE7_VITVI	Uncharacterized protein. (1199 aa)
	F6HFE8_VITVI	Uncharacterized protein. (402 aa)
	F6HG67_VITVI	Uncharacterized protein. (875 aa)
	F6HI92_VITVI	Uncharacterized protein. (1023 aa)
	F6HJE3_VITVI	Uncharacterized protein. (177 aa)
	F6HJE6_VITVI	Uncharacterized protein. (527 aa)
	F6HKC3_VITVI	Uncharacterized protein. (248 aa)
	F6HNC0_VITVI	Uncharacterized protein. (278 aa)
	F6HQ49_VITVI	S1 domain-containing protein. (330 aa)
	F6HRU1_VITVI	S4 RNA-binding domain-containing protein. (362 aa)
	F6HSJ8_VITVI	ABC transporter domain-containing protein. (157 aa)
	F6HUL5_VITVI	ELM2 domain-containing protein. (290 aa)
	F6HUW6_VITVI	Uncharacterized protein. (873 aa)
	F6HUW7_VITVI	Uncharacterized protein. (739 aa)
	F6HW96_VITVI	Uncharacterized protein. (528 aa)
	F6HWP9_VITVI	Uncharacterized protein. (1253 aa)
	F6HZ37_VITVI	CS domain-containing protein. (224 aa)
	F6I0Y4_VITVI	YL1_C domain-containing protein. (131 aa)
	F6I157_VITVI	PPR_long domain-containing protein. (1115 aa)
	F6I349_VITVI	Uncharacterized protein. (723 aa)
	F6I4L0_VITVI	Uncharacterized protein. (946 aa)
	F6I672_VITVI	ARID domain-containing protein. (635 aa)

Your Current Organism:

Vitis vinifera

NCBI taxonomy Id: 29760
Other names: V. vinifera, Vitis vinifera L., Vitis vinifera subsp. vinifera, wine grape

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
D7FBA7_VITVI	D7SWK1_VITVI	D7FBA7	D7SWK1	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Translation factor GUF1 homolog, chloroplastic; Promotes chloroplast protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes.	0.615
D7FBA7_VITVI	D7TNB0_VITVI	D7FBA7	D7TNB0	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	0.900
D7FBA7_VITVI	D7U9M6_VITVI	D7FBA7	D7U9M6	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Eukaryotic translation initiation factor 3 subunit H; Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation.	0.852
D7FBA7_VITVI	D7UBU1_VITVI	D7FBA7	D7UBU1	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Tr-type G domain-containing protein.	0.849
D7FBA7_VITVI	F6GYV6_VITVI	D7FBA7	F6GYV6	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Uncharacterized protein.	0.495
D7FBA7_VITVI	F6H2L9_VITVI	D7FBA7	F6H2L9	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	eIF-5a domain-containing protein.	0.806
D7FBA7_VITVI	F6H5P1_VITVI	D7FBA7	F6H5P1	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Translation factor GUF1 homolog, mitochondrial; Promotes mitochondrial protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Binds to mitochondrial ribosomes in a GTP-dependent manner.	0.615
D7FBA7_VITVI	F6H9P7_VITVI	D7FBA7	F6H9P7	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Uncharacterized protein.	0.660
D7FBA7_VITVI	F6HJE6_VITVI	D7FBA7	F6HJE6	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Uncharacterized protein.	0.881
D7FBA7_VITVI	F6HQ49_VITVI	D7FBA7	F6HQ49	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	S1 domain-containing protein.	0.782
D7FBA7_VITVI	F6HSJ8_VITVI	D7FBA7	F6HSJ8	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	ABC transporter domain-containing protein.	0.495
D7FBA7_VITVI	F6HW96_VITVI	D7FBA7	F6HW96	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Uncharacterized protein.	0.495
D7FBA7_VITVI	F6I6P7_VITVI	D7FBA7	F6I6P7	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	DSHCT domain-containing protein.	0.660
D7FBA7_VITVI	VITISV_010162	D7FBA7	A5AKA8	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Tr-type G domain-containing protein.	0.849
D7FBA7_VITVI	VITISV_014697	D7FBA7	A5BZP4	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Eukaryotic translation initiation factor 5A.	0.806
D7FBA7_VITVI	VITISV_018888	D7FBA7	A5B605	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Eukaryotic translation initiation factor 5A.	0.806
D7FBA7_VITVI	VITISV_020593	D7FBA7	A5C3I9	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	Eukaryotic translation initiation factor 5A.	0.806
D7SWK1_VITVI	D7FBA7_VITVI	D7SWK1	D7FBA7	Translation factor GUF1 homolog, chloroplastic; Promotes chloroplast protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes.	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	0.615
D7SWK1_VITVI	D7TNB0_VITVI	D7SWK1	D7TNB0	Translation factor GUF1 homolog, chloroplastic; Promotes chloroplast protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes.	S4 RNA-binding domain-containing protein; Belongs to the universal ribosomal protein uS4 family.	0.615
D7SWK1_VITVI	D7TUX0_VITVI	D7SWK1	D7TUX0	Translation factor GUF1 homolog, chloroplastic; Promotes chloroplast protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes.	Ribosomal_S4 domain-containing protein.	0.646