(15 nodes) Camera-type eye photoreceptor cell differentiation network (Latimeria chalumnae)

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:
	BBS4	Bardet-Biedl syndrome 4. (537 aa)
	NTRK2	Tyrosine-protein kinase receptor. (819 aa)
	CABP4	Calcium binding protein 4. (240 aa)
	NAGLU	N-acetyl-alpha-glucosaminidase. (614 aa)
	RPGRIP1	RPGR interacting protein 1. (1244 aa)
	RORB	RAR related orphan receptor B. (463 aa)
	RP1	RP1 axonemal microtubule associated. (1901 aa)
	USH1C	USH1 protein network component harmonin. (830 aa)
	BHLHE23	Basic helix-loop-helix family member e23. (224 aa)
	SOX8	SRY-box transcription factor 8. (477 aa)
	PDE6C	Phosphodiesterase. (838 aa)
	TTC8	Tetratricopeptide repeat domain 8. (534 aa)
	CNTF	Uncharacterized protein. (206 aa)
	RPGRIP1L	RPGRIP1 like. (1318 aa)
	THY1	Thy-1 cell surface antigen. (165 aa)

Your Current Organism:

Latimeria chalumnae

NCBI taxonomy Id: 7897
Other names: L. chalumnae, coelacanth

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 protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
BBS4	RPGRIP1L	ENSLACP00000002102	ENSLACP00000022895	Bardet-Biedl syndrome 4.	RPGRIP1 like.	0.475
BBS4	TTC8	ENSLACP00000002102	ENSLACP00000022744	Bardet-Biedl syndrome 4.	Tetratricopeptide repeat domain 8.	0.997
CABP4	RPGRIP1	ENSLACP00000005286	ENSLACP00000006689	Calcium binding protein 4.	RPGR interacting protein 1.	0.614
CNTF	NTRK2	ENSLACP00000022760	ENSLACP00000003030	Uncharacterized protein.	Tyrosine-protein kinase receptor.	0.436
NTRK2	CNTF	ENSLACP00000003030	ENSLACP00000022760	Tyrosine-protein kinase receptor.	Uncharacterized protein.	0.436
RPGRIP1	CABP4	ENSLACP00000006689	ENSLACP00000005286	RPGR interacting protein 1.	Calcium binding protein 4.	0.614
RPGRIP1L	BBS4	ENSLACP00000022895	ENSLACP00000002102	RPGRIP1 like.	Bardet-Biedl syndrome 4.	0.475
TTC8	BBS4	ENSLACP00000022744	ENSLACP00000002102	Tetratricopeptide repeat domain 8.	Bardet-Biedl syndrome 4.	0.997