(7 nodes) (2018) Using machine learning tools for protein database biocuration assistance. network (Takifugu rubripes)

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:
	LOC101078386	G protein-coupled receptor 158a. (1332 aa)
	LOC101079163	Rhodopsin. (349 aa)
	LOC619285	Rhodopsin. (352 aa)
	LOC778011	Rhodopsin. (353 aa)
	gprc6a	G protein-coupled receptor, class C, group 6, member A. (906 aa)
	rho	Rhodopsin. (353 aa)
	casr	Calcium-sensing receptor. (940 aa)

Your Current Organism:

Takifugu rubripes

NCBI taxonomy Id: 31033
Other names: Fugu rubripes, Sphaeroides rubripes, T. rubripes, Tetraodon rubripes, tiger puffer, torafugu

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same PNG format, but at higher resolution

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SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

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TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

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TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

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structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

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node degree of proteins in your network (given the current score cut-off)

... network coordinates:

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a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

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MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

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a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

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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
LOC101078386	casr	ENSTRUP00000058864	ENSTRUP00000043231	G protein-coupled receptor 158a.	Calcium-sensing receptor.	0.578
LOC101078386	gprc6a	ENSTRUP00000058864	ENSTRUP00000017430	G protein-coupled receptor 158a.	G protein-coupled receptor, class C, group 6, member A.	0.685
LOC619285	LOC778011	ENSTRUP00000005472	ENSTRUP00000010753	Rhodopsin.	Rhodopsin.	0.932
LOC619285	rho	ENSTRUP00000005472	ENSTRUP00000026809	Rhodopsin.	Rhodopsin.	0.932
LOC778011	LOC619285	ENSTRUP00000010753	ENSTRUP00000005472	Rhodopsin.	Rhodopsin.	0.932
LOC778011	rho	ENSTRUP00000010753	ENSTRUP00000026809	Rhodopsin.	Rhodopsin.	0.935
casr	LOC101078386	ENSTRUP00000043231	ENSTRUP00000058864	Calcium-sensing receptor.	G protein-coupled receptor 158a.	0.578
casr	gprc6a	ENSTRUP00000043231	ENSTRUP00000017430	Calcium-sensing receptor.	G protein-coupled receptor, class C, group 6, member A.	0.910
gprc6a	LOC101078386	ENSTRUP00000017430	ENSTRUP00000058864	G protein-coupled receptor, class C, group 6, member A.	G protein-coupled receptor 158a.	0.685
gprc6a	casr	ENSTRUP00000017430	ENSTRUP00000043231	G protein-coupled receptor, class C, group 6, member A.	Calcium-sensing receptor.	0.910
rho	LOC619285	ENSTRUP00000026809	ENSTRUP00000005472	Rhodopsin.	Rhodopsin.	0.932
rho	LOC778011	ENSTRUP00000026809	ENSTRUP00000010753	Rhodopsin.	Rhodopsin.	0.935