(7 nodes) Paraxial mesoderm development 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:
	LEF1	Lymphoid enhancer binding factor 1. (397 aa)
	POGLUT1	Protein O-glucosyltransferase 1. (351 aa)
	SMAD3	Mothers against decapentaplegic homolog. (358 aa)
	NUP133	Nucleoporin 133; Belongs to the actin family. (1421 aa)
	EPB41L5	Erythrocyte membrane protein band 4.1 like 5. (506 aa)
	EXOC4	Exocyst complex component 4. (480 aa)
	SMAD2	Mothers against decapentaplegic homolog. (467 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 proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
LEF1	SMAD2	ENSLACP00000005598	ENSLACP00000008339	Lymphoid enhancer binding factor 1.	Mothers against decapentaplegic homolog.	0.506
LEF1	SMAD3	ENSLACP00000005598	ENSLACP00000011989	Lymphoid enhancer binding factor 1.	Mothers against decapentaplegic homolog.	0.506
SMAD2	LEF1	ENSLACP00000008339	ENSLACP00000005598	Mothers against decapentaplegic homolog.	Lymphoid enhancer binding factor 1.	0.506
SMAD2	SMAD3	ENSLACP00000008339	ENSLACP00000011989	Mothers against decapentaplegic homolog.	Mothers against decapentaplegic homolog.	0.901
SMAD3	LEF1	ENSLACP00000011989	ENSLACP00000005598	Mothers against decapentaplegic homolog.	Lymphoid enhancer binding factor 1.	0.506
SMAD3	SMAD2	ENSLACP00000011989	ENSLACP00000008339	Mothers against decapentaplegic homolog.	Mothers against decapentaplegic homolog.	0.901