(47 nodes) Endochondral bone morphogenesis network (Tursiops truncatus)

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:
	COL3A1	Collagen alpha-1(III) chain. (1464 aa)
	RARA	Retinoic acid receptor alpha-like. (618 aa)
	BMP6	Bone morphogenetic protein 6. (304 aa)
	BMPR1B	Serine/threonine-protein kinase receptor; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily. (502 aa)
	COL13A1	Collagen alpha-1(XIII) chain. (713 aa)
	EXT1	Exostosin-1; Belongs to the glycosyltransferase 47 family. (746 aa)
	NAB2	NGFI-A binding protein 2. (488 aa)
	IMPAD1	Inositol monophosphatase 3 isoform X1. (358 aa)
	SERPINH1	Serpin H1; Belongs to the serpin family. (418 aa)
	TRPV4	Transient receptor potential cation channel subfamily V member 4-like. (591 aa)
	RARB	Retinoic acid receptor beta. (522 aa)
	BMP4	Bone morphogenetic protein 4. (407 aa)
	AXIN2	Axin-2-like. (839 aa)
	THBS3	Thrombospondin 3. (956 aa)
	LOC109547947	Cystathionine beta-synthase-like. (561 aa)
	IHH	Indian hedgehog protein. (409 aa)
	MATN1	Cartilage matrix protein. (494 aa)
	COMP	Cartilage oligomeric matrix protein. (756 aa)
	IFT80	Intraflagellar transport protein 80 homolog isoform X2. (777 aa)
	ATF2	Cyclic AMP-dependent transcription factor ATF-2 isoform X1. (505 aa)
	ALPL	Alkaline phosphatase. (520 aa)
	ANXA6	Annexin. (722 aa)
	COL2A1	Collagen type II alpha 1 chain. (1487 aa)
	MEF2D	Myocyte enhancer factor 2D. (494 aa)
	CSGALNACT1	Hexosyltransferase. (526 aa)
	MMP14	Matrix metallopeptidase 14. (582 aa)
	SHOX2	LOW QUALITY PROTEIN: short stature homeobox protein 2. (282 aa)
	PHOSPHO2	Pyridoxal phosphate phosphatase PHOSPHO2. (241 aa)
	MMP13	Collagenase 3. (438 aa)
	PEX7	Peroxisomal biogenesis factor 7. (299 aa)
	RARG	Retinoic acid receptor beta. (453 aa)
	EXT2	Exostosin-2 isoform X3; Belongs to the glycosyltransferase 47 family. (726 aa)
	MMP16	Matrix metalloproteinase-16. (606 aa)
	HOXA11	Homeobox protein Hox-A11. (311 aa)
	MEF2C	Myocyte-specific enhancer factor 2C isoform X1. (472 aa)
	PHOSPHO1	LOW QUALITY PROTEIN: phosphoethanolamine/phosphocholine phosphatase. (267 aa)
	COL1A1	Collagen type I alpha 1 chain. (1462 aa)
	SOX9	Transcription factor SOX-9. (509 aa)
	ZMPSTE24	CAAX prenyl protease; Proteolytically removes the C-terminal three residues of farnesylated proteins; Belongs to the peptidase M48A family. (475 aa)
	SCX	Scleraxis bHLH transcription factor. (203 aa)
	SCUBE2	Signal peptide, CUB and EGF-like domain-containing protein 2 isoform X1. (995 aa)
	RUNX2	Runt-related transcription factor; Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'- TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. (587 aa)
	DLX5	Homeobox protein DLX-5. (289 aa)
	CER1	Cerberus. (271 aa)
	TRIP11	Thyroid receptor-interacting protein 11 isoform X1. (1979 aa)
	FGF18	Fibroblast growth factor 18; Belongs to the heparin-binding growth factors family. (207 aa)
	NPPC	Natriuretic peptide C. (126 aa)

Your Current Organism:

Tursiops truncatus

NCBI taxonomy Id: 9739
Other names: Atlantic bottlenose dolphin, T. truncatus, bottle-nosed dolphin, common bottlenose dolphin

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
ALPL	COL1A1	ENSTTRP00000000449	ENSTTRP00000005185	Alkaline phosphatase.	Collagen type I alpha 1 chain.	0.682
ALPL	COL2A1	ENSTTRP00000000449	ENSTTRP00000000695	Alkaline phosphatase.	Collagen type II alpha 1 chain.	0.648
ALPL	DLX5	ENSTTRP00000000449	ENSTTRP00000007188	Alkaline phosphatase.	Homeobox protein DLX-5.	0.491
ALPL	IHH	ENSTTRP00000000449	ENSTTRP00000009502	Alkaline phosphatase.	Indian hedgehog protein.	0.416
ALPL	MMP13	ENSTTRP00000000449	ENSTTRP00000002042	Alkaline phosphatase.	Collagenase 3.	0.414
ALPL	PHOSPHO1	ENSTTRP00000000449	ENSTTRP00000004373	Alkaline phosphatase.	LOW QUALITY PROTEIN: phosphoethanolamine/phosphocholine phosphatase.	0.508
ALPL	RUNX2	ENSTTRP00000000449	ENSTTRP00000006566	Alkaline phosphatase.	Runt-related transcription factor; Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'- TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX.	0.762
ALPL	SOX9	ENSTTRP00000000449	ENSTTRP00000005370	Alkaline phosphatase.	Transcription factor SOX-9.	0.537
ALPL	TRIP11	ENSTTRP00000000449	ENSTTRP00000007661	Alkaline phosphatase.	Thyroid receptor-interacting protein 11 isoform X1.	0.582
ANXA6	LOC109547947	ENSTTRP00000000467	ENSTTRP00000009428	Annexin.	Cystathionine beta-synthase-like.	0.420
AXIN2	BMP4	ENSTTRP00000008850	ENSTTRP00000008787	Axin-2-like.	Bone morphogenetic protein 4.	0.554
AXIN2	RUNX2	ENSTTRP00000008850	ENSTTRP00000006566	Axin-2-like.	Runt-related transcription factor; Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'- TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX.	0.525
AXIN2	SOX9	ENSTTRP00000008850	ENSTTRP00000005370	Axin-2-like.	Transcription factor SOX-9.	0.560
BMP4	AXIN2	ENSTTRP00000008787	ENSTTRP00000008850	Bone morphogenetic protein 4.	Axin-2-like.	0.554
BMP4	BMP6	ENSTTRP00000008787	ENSTTRP00000015103	Bone morphogenetic protein 4.	Bone morphogenetic protein 6.	0.955
BMP4	BMPR1B	ENSTTRP00000008787	ENSTTRP00000014265	Bone morphogenetic protein 4.	Serine/threonine-protein kinase receptor; Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. TGFB receptor subfamily.	0.997
BMP4	CER1	ENSTTRP00000008787	ENSTTRP00000007603	Bone morphogenetic protein 4.	Cerberus.	0.568
BMP4	COL1A1	ENSTTRP00000008787	ENSTTRP00000005185	Bone morphogenetic protein 4.	Collagen type I alpha 1 chain.	0.558
BMP4	COL2A1	ENSTTRP00000008787	ENSTTRP00000000695	Bone morphogenetic protein 4.	Collagen type II alpha 1 chain.	0.481
BMP4	DLX5	ENSTTRP00000008787	ENSTTRP00000007188	Bone morphogenetic protein 4.	Homeobox protein DLX-5.	0.697