(31 nodes) Entrainment of circadian clock by photoperiod network (Physeter catodon)

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:
	CRY2	Cryptochrome-2. (614 aa)
	ENSPCTP00005002086	annotation not available (309 aa)
	PER3	Period circadian protein homolog 3 isoform X7. (491 aa)
	PER3-2	Period circadian protein homolog 3 isoform X6. (502 aa)
	ATOH7	Protein atonal homolog 7. (152 aa)
	CRY1	Cryptochrome-1 isoform X1. (587 aa)
	PPP1CB	Serine/threonine-protein phosphatase; Belongs to the PPP phosphatase family. (327 aa)
	RBM4B	RNA-binding protein 4B isoform X2. (359 aa)
	OPN5	Opsin-5; Belongs to the G-protein coupled receptor 1 family. (383 aa)
	FBXL6	F-box/LRR-repeat protein 6 isoform X1. (535 aa)
	PDE6B	Phosphodiesterase. (854 aa)
	FBXL3	F-box/LRR-repeat protein 3 isoform X1. (429 aa)
	BHLHE40	Class E basic helix-loop-helix protein 40. (412 aa)
	PER2	Period circadian protein homolog 2 isoform X1. (1207 aa)
	CRTC1	CREB-regulated transcription coactivator 1. (612 aa)
	FBXL22	F-box and leucine-rich protein 22. (128 aa)
	FBXL21P	F-box/LRR-repeat protein 21. (434 aa)
	PER1	Period circadian protein homolog 1 isoform X1. (1278 aa)
	ID2	DNA-binding protein inhibitor ID-2. (134 aa)
	TP53	Cellular tumor antigen p53; Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression; Belongs to the p53 family. (387 aa)
	PML	Protein PML isoform X1. (870 aa)
	LOC102988511	Serine/threonine-protein kinase SIK1 isoform X1. (785 aa)
	FBXL8	F-box/LRR-repeat protein 8 isoform X2. (343 aa)
	ENSPCTP00005025701	annotation not available (138 aa)
	RBM4	RNA-binding protein 4 isoform X1. (363 aa)
	FBXL17	F-box/LRR-repeat protein 17. (697 aa)
	PPP1CC	Serine/threonine-protein phosphatase; Belongs to the PPP phosphatase family. (337 aa)
	FBXL12	F-box/LRR-repeat protein 12 isoform X1. (326 aa)
	USP2	Ubiquitin carboxyl-terminal hydrolase; Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes. Belongs to the peptidase C19 family. (603 aa)
	NR2F6	Nuclear receptor subfamily 2 group F member 6 isoform X1. (413 aa)
	PPP1CA	Serine/threonine-protein phosphatase; Belongs to the PPP phosphatase family. (330 aa)

Your Current Organism:

Physeter catodon

NCBI taxonomy Id: 9755
Other names: P. catodon, Physeter macrocephalus, sperm whale

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
BHLHE40	CRY1	ENSPCTP00005015149	ENSPCTP00005007329	Class E basic helix-loop-helix protein 40.	Cryptochrome-1 isoform X1.	0.479
BHLHE40	CRY2	ENSPCTP00005015149	ENSPCTP00005022830	Class E basic helix-loop-helix protein 40.	Cryptochrome-2.	0.422
BHLHE40	PER1	ENSPCTP00005015149	ENSPCTP00005018567	Class E basic helix-loop-helix protein 40.	Period circadian protein homolog 1 isoform X1.	0.407
BHLHE40	PER2	ENSPCTP00005015149	ENSPCTP00005015199	Class E basic helix-loop-helix protein 40.	Period circadian protein homolog 2 isoform X1.	0.471
BHLHE40	PER3	ENSPCTP00005015149	ENSPCTP00005005745	Class E basic helix-loop-helix protein 40.	Period circadian protein homolog 3 isoform X7.	0.414
BHLHE40	PER3-2	ENSPCTP00005015149	ENSPCTP00005005767	Class E basic helix-loop-helix protein 40.	Period circadian protein homolog 3 isoform X6.	0.414
CRY1	BHLHE40	ENSPCTP00005007329	ENSPCTP00005015149	Cryptochrome-1 isoform X1.	Class E basic helix-loop-helix protein 40.	0.479
CRY1	CRY2	ENSPCTP00005007329	ENSPCTP00005022830	Cryptochrome-1 isoform X1.	Cryptochrome-2.	0.996
CRY1	FBXL12	ENSPCTP00005007329	ENSPCTP00005028416	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 12 isoform X1.	0.460
CRY1	FBXL17	ENSPCTP00005007329	ENSPCTP00005026726	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 17.	0.460
CRY1	FBXL21P	ENSPCTP00005007329	ENSPCTP00005017117	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 21.	0.739
CRY1	FBXL22	ENSPCTP00005007329	ENSPCTP00005016835	Cryptochrome-1 isoform X1.	F-box and leucine-rich protein 22.	0.453
CRY1	FBXL3	ENSPCTP00005007329	ENSPCTP00005013849	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 3 isoform X1.	0.994
CRY1	FBXL6	ENSPCTP00005007329	ENSPCTP00005013076	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 6 isoform X1.	0.460
CRY1	FBXL8	ENSPCTP00005007329	ENSPCTP00005022158	Cryptochrome-1 isoform X1.	F-box/LRR-repeat protein 8 isoform X2.	0.453
CRY1	PER1	ENSPCTP00005007329	ENSPCTP00005018567	Cryptochrome-1 isoform X1.	Period circadian protein homolog 1 isoform X1.	0.846
CRY1	PER2	ENSPCTP00005007329	ENSPCTP00005015199	Cryptochrome-1 isoform X1.	Period circadian protein homolog 2 isoform X1.	0.991
CRY1	PER3	ENSPCTP00005007329	ENSPCTP00005005745	Cryptochrome-1 isoform X1.	Period circadian protein homolog 3 isoform X7.	0.917
CRY1	PER3-2	ENSPCTP00005007329	ENSPCTP00005005767	Cryptochrome-1 isoform X1.	Period circadian protein homolog 3 isoform X6.	0.917
CRY2	BHLHE40	ENSPCTP00005022830	ENSPCTP00005015149	Cryptochrome-2.	Class E basic helix-loop-helix protein 40.	0.422