(10 nodes) Pentatricopeptide repeat network (Xiphophorus maculatus)

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:
	DENND4A	DENN domain containing 4A. (1970 aa)
	dennd4b	DENN/MADD domain containing 4B. (1505 aa)
	ptcd3	Pentatricopeptide repeat domain 3. (542 aa)
	polrmt	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family. (1321 aa)
	LOC102221245	Pentatricopeptide repeat domain 1. (691 aa)
	mrps27	Mitochondrial ribosomal protein S27. (417 aa)
	lrpprc	Leucine-rich pentatricopeptide repeat containing. (1415 aa)
	dennd4a	DENN/MADD domain containing 4A. (1685 aa)
	dennd4c	DENN/MADD domain containing 4C. (1910 aa)
	ptcd2	Pentatricopeptide repeat domain 2. (421 aa)

Your Current Organism:

Xiphophorus maculatus

NCBI taxonomy Id: 8083
Other names: Platypoecilus maculatus, X. maculatus, southern platyfish

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
LOC102221245	polrmt	ENSXMAP00000015564	ENSXMAP00000012490	Pentatricopeptide repeat domain 1.	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	0.598
LOC102221245	ptcd3	ENSXMAP00000015564	ENSXMAP00000004036	Pentatricopeptide repeat domain 1.	Pentatricopeptide repeat domain 3.	0.410
lrpprc	polrmt	ENSXMAP00000018156	ENSXMAP00000012490	Leucine-rich pentatricopeptide repeat containing.	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	0.560
lrpprc	ptcd3	ENSXMAP00000018156	ENSXMAP00000004036	Leucine-rich pentatricopeptide repeat containing.	Pentatricopeptide repeat domain 3.	0.725
mrps27	ptcd3	ENSXMAP00000016146	ENSXMAP00000004036	Mitochondrial ribosomal protein S27.	Pentatricopeptide repeat domain 3.	0.992
polrmt	LOC102221245	ENSXMAP00000012490	ENSXMAP00000015564	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	Pentatricopeptide repeat domain 1.	0.598
polrmt	lrpprc	ENSXMAP00000012490	ENSXMAP00000018156	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	Leucine-rich pentatricopeptide repeat containing.	0.560
polrmt	ptcd3	ENSXMAP00000012490	ENSXMAP00000004036	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	Pentatricopeptide repeat domain 3.	0.573
ptcd3	LOC102221245	ENSXMAP00000004036	ENSXMAP00000015564	Pentatricopeptide repeat domain 3.	Pentatricopeptide repeat domain 1.	0.410
ptcd3	lrpprc	ENSXMAP00000004036	ENSXMAP00000018156	Pentatricopeptide repeat domain 3.	Leucine-rich pentatricopeptide repeat containing.	0.725
ptcd3	mrps27	ENSXMAP00000004036	ENSXMAP00000016146	Pentatricopeptide repeat domain 3.	Mitochondrial ribosomal protein S27.	0.992
ptcd3	polrmt	ENSXMAP00000004036	ENSXMAP00000012490	Pentatricopeptide repeat domain 3.	DNA-directed RNA polymerase; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the phage and mitochondrial RNA polymerase family.	0.573