(22 nodes) Neuron fate specification network (Oreochromis niloticus)

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:
	LOC100692597	Peptidylprolyl isomerase. (467 aa)
	lhx4	LIM homeobox 4. (472 aa)
	I3J0L4_ORENI	T-box transcription factor 2a. (621 aa)
	ISL2	ISL LIM homeobox 2b. (364 aa)
	gsx2	GS homeobox 2. (238 aa)
	fkbp8	Peptidylprolyl isomerase. (403 aa)
	LOC100704844	Uncharacterized protein. (477 aa)
	shh	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development. (415 aa)
	mnx1	Motor neuron and pancreas homeobox 1. (315 aa)
	LOC100690382	Homeobox C10a. (331 aa)
	LOC100691488	Fibroblast growth factor; Belongs to the heparin-binding growth factors family. (207 aa)
	LOC100700683	ISL LIM homeobox 1. (351 aa)
	lhx9	LIM homeobox 9. (476 aa)
	LHX3	LIM homeobox 3. (400 aa)
	ISL2-2	ISL LIM homeobox 2a. (363 aa)
	zc4h2	Zinc finger, C4H2 domain containing. (224 aa)
	lhx2	LIM homeobox 2b. (417 aa)
	TBX2	T-box transcription factor 2. (739 aa)
	mib1	Mindbomb E3 ubiquitin protein ligase 1. (1040 aa)
	LOC100694496	Motor neuron and pancreas homeobox 2a. (323 aa)
	dlx3	Distal-less homeobox 3b. (281 aa)
	I3KNU7_ORENI	Fibroblast growth factor; Belongs to the heparin-binding growth factors family. (262 aa)

Your Current Organism:

Oreochromis niloticus

NCBI taxonomy Id: 8128
Other names: Nile tilapia, O. niloticus, Oreochromis nilotica, Tilapia nilotica

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
I3KNU7_ORENI	LOC100691488	ENSONIP00000050554	ENSONIP00000016574	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.822
I3KNU7_ORENI	shh	ENSONIP00000050554	ENSONIP00000007484	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.528
ISL2	LHX3	ENSONIP00000003151	ENSONIP00000018860	ISL LIM homeobox 2b.	LIM homeobox 3.	0.766
ISL2	lhx4	ENSONIP00000003151	ENSONIP00000002400	ISL LIM homeobox 2b.	LIM homeobox 4.	0.757
ISL2-2	LHX3	ENSONIP00000019199	ENSONIP00000018860	ISL LIM homeobox 2a.	LIM homeobox 3.	0.757
ISL2-2	lhx4	ENSONIP00000019199	ENSONIP00000002400	ISL LIM homeobox 2a.	LIM homeobox 4.	0.757
LHX3	ISL2	ENSONIP00000018860	ENSONIP00000003151	LIM homeobox 3.	ISL LIM homeobox 2b.	0.766
LHX3	ISL2-2	ENSONIP00000018860	ENSONIP00000019199	LIM homeobox 3.	ISL LIM homeobox 2a.	0.757
LHX3	LOC100700683	ENSONIP00000018860	ENSONIP00000017528	LIM homeobox 3.	ISL LIM homeobox 1.	0.757
LOC100691488	I3KNU7_ORENI	ENSONIP00000016574	ENSONIP00000050554	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.822
LOC100691488	dlx3	ENSONIP00000016574	ENSONIP00000045287	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Distal-less homeobox 3b.	0.437
LOC100691488	shh	ENSONIP00000016574	ENSONIP00000007484	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.599
LOC100700683	LHX3	ENSONIP00000017528	ENSONIP00000018860	ISL LIM homeobox 1.	LIM homeobox 3.	0.757
LOC100700683	gsx2	ENSONIP00000017528	ENSONIP00000003784	ISL LIM homeobox 1.	GS homeobox 2.	0.478
LOC100700683	lhx4	ENSONIP00000017528	ENSONIP00000002400	ISL LIM homeobox 1.	LIM homeobox 4.	0.757
dlx3	LOC100691488	ENSONIP00000045287	ENSONIP00000016574	Distal-less homeobox 3b.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.437
gsx2	LOC100700683	ENSONIP00000003784	ENSONIP00000017528	GS homeobox 2.	ISL LIM homeobox 1.	0.478
lhx4	ISL2	ENSONIP00000002400	ENSONIP00000003151	LIM homeobox 4.	ISL LIM homeobox 2b.	0.757
lhx4	ISL2-2	ENSONIP00000002400	ENSONIP00000019199	LIM homeobox 4.	ISL LIM homeobox 2a.	0.757
lhx4	LOC100700683	ENSONIP00000002400	ENSONIP00000017528	LIM homeobox 4.	ISL LIM homeobox 1.	0.757