(12 nodes) (2018) Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face. 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:
	PAX6	Paired box 6. (463 aa)
	PAX2	Paired box 2. (456 aa)
	BMP4	Bone morphogenetic protein 4. (460 aa)
	RUNX2	Runt-related transcription factor. (452 aa)
	SHH	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development. (421 aa)
	PAX1	Paired box 1. (362 aa)
	TBX15	T-box transcription factor 15. (566 aa)
	SOX2	SRY-box transcription factor 2. (315 aa)
	EDAR	Ectodysplasin A receptor. (454 aa)
	GLI3	GLI family zinc finger 3. (1456 aa)
	DCHS2	Uncharacterized protein. (3211 aa)
	SIX3	SIX homeobox 3. (291 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
BMP4	EDAR	ENSLACP00000021723	ENSLACP00000004634	Bone morphogenetic protein 4.	Ectodysplasin A receptor.	0.672
BMP4	GLI3	ENSLACP00000021723	ENSLACP00000004224	Bone morphogenetic protein 4.	GLI family zinc finger 3.	0.444
BMP4	PAX6	ENSLACP00000021723	ENSLACP00000017411	Bone morphogenetic protein 4.	Paired box 6.	0.404
BMP4	RUNX2	ENSLACP00000021723	ENSLACP00000013109	Bone morphogenetic protein 4.	Runt-related transcription factor.	0.675
BMP4	SHH	ENSLACP00000021723	ENSLACP00000013019	Bone morphogenetic protein 4.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.760
BMP4	SOX2	ENSLACP00000021723	ENSLACP00000007400	Bone morphogenetic protein 4.	SRY-box transcription factor 2.	0.477
DCHS2	PAX1	ENSLACP00000002837	ENSLACP00000010922	Uncharacterized protein.	Paired box 1.	0.438
DCHS2	TBX15	ENSLACP00000002837	ENSLACP00000008697	Uncharacterized protein.	T-box transcription factor 15.	0.501
EDAR	BMP4	ENSLACP00000004634	ENSLACP00000021723	Ectodysplasin A receptor.	Bone morphogenetic protein 4.	0.672
EDAR	RUNX2	ENSLACP00000004634	ENSLACP00000013109	Ectodysplasin A receptor.	Runt-related transcription factor.	0.461
EDAR	SHH	ENSLACP00000004634	ENSLACP00000013019	Ectodysplasin A receptor.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.548
EDAR	TBX15	ENSLACP00000004634	ENSLACP00000008697	Ectodysplasin A receptor.	T-box transcription factor 15.	0.431
GLI3	BMP4	ENSLACP00000004224	ENSLACP00000021723	GLI family zinc finger 3.	Bone morphogenetic protein 4.	0.444
GLI3	PAX6	ENSLACP00000004224	ENSLACP00000017411	GLI family zinc finger 3.	Paired box 6.	0.485
GLI3	RUNX2	ENSLACP00000004224	ENSLACP00000013109	GLI family zinc finger 3.	Runt-related transcription factor.	0.425
GLI3	SHH	ENSLACP00000004224	ENSLACP00000013019	GLI family zinc finger 3.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.702
PAX1	DCHS2	ENSLACP00000010922	ENSLACP00000002837	Paired box 1.	Uncharacterized protein.	0.438
PAX1	TBX15	ENSLACP00000010922	ENSLACP00000008697	Paired box 1.	T-box transcription factor 15.	0.400
PAX2	RUNX2	ENSLACP00000019870	ENSLACP00000013109	Paired box 2.	Runt-related transcription factor.	0.471
PAX2	SHH	ENSLACP00000019870	ENSLACP00000013019	Paired box 2.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.456