(26 nodes) Hindlimb morphogenesis network (Ursus americanus)

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:
	RARG	Retinoic acid receptor gamma. (458 aa)
	TP63	Tumor protein 63 (p63); Acts as a sequence specific DNA binding transcriptional activator or repressor. The isoforms contain a varying set of transactivation and auto-regulating transactivation inhibiting domains thus showing an isoform specific activity. May be required in conjunction with TP73/p73 for initiation of p53/TP53 dependent apoptosis in response to genotoxic insults and the presence of activated oncogenes. (680 aa)
	OSR1	Odd-skipped related transcription factor 1. (267 aa)
	NOTCH1	Notch receptor 1. (2547 aa)
	MED1	Mediator of RNA polymerase II transcription subunit 1; Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. (1477 aa)
	CHD7	Chromodomain helicase DNA binding protein 7. (2987 aa)
	HOXD9	Homeobox D9. (341 aa)
	HOXD10	Homeobox D10. (410 aa)
	FGF4	Fibroblast growth factor; Belongs to the heparin-binding growth factors family. (197 aa)
	TFAP2B	Transcription factor AP-2 beta. (460 aa)
	BMP4	Bone morphogenetic protein 4. (409 aa)
	ALX3	ALX homeobox 3. (341 aa)
	OSR2	Odd-skipped related transciption factor 2. (312 aa)
	PITX1	Homeobox protein. (313 aa)
	GPC3	Glypican 3; Cell surface proteoglycan that bears heparan sulfate. Belongs to the glypican family. (496 aa)
	ENSUAMP00000017830	Uncharacterized protein. (157 aa)
	RPGRIP1L	RPGRIP1 like. (1207 aa)
	RARB	Retinoic acid receptor beta. (336 aa)
	ZBTB16	Zinc finger and BTB domain containing 16. (423 aa)
	GDF5	Growth differentiation factor 5. (499 aa)
	PTCH1	Patched 1. (1453 aa)
	BMPR1A	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily. (532 aa)
	ENSUAMP00000000600	Uncharacterized protein. (130 aa)
	MSX1	Msh homeobox 1. (303 aa)
	TBX4	T-box transcription factor 4. (529 aa)
	ALX4	ALX homeobox 4. (408 aa)

Your Current Organism:

Ursus americanus

NCBI taxonomy Id: 9643
Other names: American black bear, Euarctos americanus, U. americanus

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	BMPR1A	ENSUAMP00000028868	ENSUAMP00000036181	Bone morphogenetic protein 4.	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	0.997
BMP4	ENSUAMP00000000600	ENSUAMP00000028868	ENSUAMP00000000600	Bone morphogenetic protein 4.	Uncharacterized protein.	0.428
BMP4	ENSUAMP00000017830	ENSUAMP00000028868	ENSUAMP00000017830	Bone morphogenetic protein 4.	Uncharacterized protein.	0.428
BMP4	FGF4	ENSUAMP00000028868	ENSUAMP00000032522	Bone morphogenetic protein 4.	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	0.649
BMP4	GDF5	ENSUAMP00000028868	ENSUAMP00000009595	Bone morphogenetic protein 4.	Growth differentiation factor 5.	0.454
BMP4	GPC3	ENSUAMP00000028868	ENSUAMP00000021714	Bone morphogenetic protein 4.	Glypican 3; Cell surface proteoglycan that bears heparan sulfate. Belongs to the glypican family.	0.429
BMP4	MSX1	ENSUAMP00000028868	ENSUAMP00000000613	Bone morphogenetic protein 4.	Msh homeobox 1.	0.628
BMP4	NOTCH1	ENSUAMP00000028868	ENSUAMP00000034225	Bone morphogenetic protein 4.	Notch receptor 1.	0.426
BMP4	PTCH1	ENSUAMP00000028868	ENSUAMP00000007757	Bone morphogenetic protein 4.	Patched 1.	0.528
BMPR1A	BMP4	ENSUAMP00000036181	ENSUAMP00000028868	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	Bone morphogenetic protein 4.	0.997
BMPR1A	GDF5	ENSUAMP00000036181	ENSUAMP00000009595	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	Growth differentiation factor 5.	0.995
BMPR1A	MSX1	ENSUAMP00000036181	ENSUAMP00000000613	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	Msh homeobox 1.	0.636
ENSUAMP00000000600	BMP4	ENSUAMP00000000600	ENSUAMP00000028868	Uncharacterized protein.	Bone morphogenetic protein 4.	0.428
ENSUAMP00000000600	ENSUAMP00000017830	ENSUAMP00000000600	ENSUAMP00000017830	Uncharacterized protein.	Uncharacterized protein.	0.671
ENSUAMP00000017830	BMP4	ENSUAMP00000017830	ENSUAMP00000028868	Uncharacterized protein.	Bone morphogenetic protein 4.	0.428
ENSUAMP00000017830	ENSUAMP00000000600	ENSUAMP00000017830	ENSUAMP00000000600	Uncharacterized protein.	Uncharacterized protein.	0.671
FGF4	BMP4	ENSUAMP00000032522	ENSUAMP00000028868	Fibroblast growth factor; Belongs to the heparin-binding growth factors family.	Bone morphogenetic protein 4.	0.649
GDF5	BMP4	ENSUAMP00000009595	ENSUAMP00000028868	Growth differentiation factor 5.	Bone morphogenetic protein 4.	0.454
GDF5	BMPR1A	ENSUAMP00000009595	ENSUAMP00000036181	Growth differentiation factor 5.	Receptor protein serine/threonine kinase; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	0.995
GPC3	BMP4	ENSUAMP00000021714	ENSUAMP00000028868	Glypican 3; Cell surface proteoglycan that bears heparan sulfate. Belongs to the glypican family.	Bone morphogenetic protein 4.	0.429