(9 nodes) (2013) Cortical plasticity within and across lifetimes: how can development inform us about phenotypic transformations? network (Saimiri boliviensis)

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:
	HDAC9	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. (1066 aa)
	HOXD13	Homeobox D13. (322 aa)
	PAX6	Paired box 6. (488 aa)
	HDAC7	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. (1000 aa)
	NR3C1	Glucocorticoid receptor; Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription factor that binds to glucocorticoid response elements (GRE), both for nuclear and mitochondrial DNA, and as a modulator of other transcription factors. Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Involved in chromatin remodeling. Plays a role in rapid mRNA degradation by binding to the 5' UTR of target mRNAs and interacting with PNRC2 in a ligand-dependent manner which recruits the RNA helicase UPF1 and the mRNA-decapping enzyme DCP [...] (777 aa)
	EMX2	Empty spiracles homeobox 2. (225 aa)
	HDAC4	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. (1090 aa)
	FGF8	Fibroblast growth factor; Belongs to the heparin-binding growth factors family. (233 aa)
	HDAC5	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. (1088 aa)

Your Current Organism:

Saimiri boliviensis

NCBI taxonomy Id: 39432
Other names: Bolivian squirrel monkey, S. boliviensis boliviensis, Saimiri boliviensis boliviensis

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
EMX2	FGF8	ENSSBOP00000004516	ENSSBOP00000020648	Empty spiracles homeobox 2.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.513
EMX2	HDAC9	ENSSBOP00000004516	ENSSBOP00000011952	Empty spiracles homeobox 2.	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	0.587
EMX2	HOXD13	ENSSBOP00000004516	ENSSBOP00000032778	Empty spiracles homeobox 2.	Homeobox D13.	0.794
EMX2	PAX6	ENSSBOP00000004516	ENSSBOP00000001518	Empty spiracles homeobox 2.	Paired box 6.	0.437
FGF8	EMX2	ENSSBOP00000020648	ENSSBOP00000004516	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Empty spiracles homeobox 2.	0.513
FGF8	HOXD13	ENSSBOP00000020648	ENSSBOP00000032778	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Homeobox D13.	0.583
FGF8	PAX6	ENSSBOP00000020648	ENSSBOP00000001518	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Paired box 6.	0.538
HDAC4	HDAC5	ENSSBOP00000021361	ENSSBOP00000019829	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	0.934
HDAC5	HDAC4	ENSSBOP00000019829	ENSSBOP00000021361	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	0.934
HDAC9	EMX2	ENSSBOP00000011952	ENSSBOP00000004516	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	Empty spiracles homeobox 2.	0.587
HDAC9	HOXD13	ENSSBOP00000011952	ENSSBOP00000032778	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	Homeobox D13.	0.592
HOXD13	EMX2	ENSSBOP00000032778	ENSSBOP00000004516	Homeobox D13.	Empty spiracles homeobox 2.	0.794
HOXD13	FGF8	ENSSBOP00000032778	ENSSBOP00000020648	Homeobox D13.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.583
HOXD13	HDAC9	ENSSBOP00000032778	ENSSBOP00000011952	Homeobox D13.	Histone deacetylase; Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.	0.592
HOXD13	PAX6	ENSSBOP00000032778	ENSSBOP00000001518	Homeobox D13.	Paired box 6.	0.732
PAX6	EMX2	ENSSBOP00000001518	ENSSBOP00000004516	Paired box 6.	Empty spiracles homeobox 2.	0.437
PAX6	FGF8	ENSSBOP00000001518	ENSSBOP00000020648	Paired box 6.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.538
PAX6	HOXD13	ENSSBOP00000001518	ENSSBOP00000032778	Paired box 6.	Homeobox D13.	0.732