(16 nodes) (2018) A transcription factor collective defines the HSN serotonergic neuron regulatory landscape. network (Caenorhabditis briggsae)

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:
	flp-19	Protein CBR-FLP-19. (89 aa)
	nlp-3	Protein CBR-NLP-3. (91 aa)
	nlg-1	Protein CBR-NLG-1. (800 aa)
	ida-1	Protein CBR-IDA-1. (722 aa)
	bas-1	Protein CBR-BAS-1. (514 aa)
	sem-4	Protein CBR-SEM-4. (739 aa)
	lgc-55	Protein CBR-LGC-55; Belongs to the ligand-gated ion channel (TC 1.A.9) family. (538 aa)
	egl-18	Protein CBR-EGL-18. (419 aa)
	unc-40	Protein CBR-UNC-40. (1407 aa)
	unc-86	POU domain protein. (346 aa)
	egl-46	Protein CBR-EGL-46. (283 aa)
	lin-41	Protein CBR-LIN-41. (934 aa)
	ttx-3	Protein CBR-TTX-3. (380 aa)
	rrf-3	Protein CBR-RRF-3. (1766 aa)
	rol-6	Protein CBR-ROL-6. (348 aa)
	rab-3	Protein CBR-RAB-3. (219 aa)

Your Current Organism:

Caenorhabditis briggsae

NCBI taxonomy Id: 6238
Other names: C. briggsae, Caenorhabditis briggsae AF16

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
bas-1	egl-46	A8X844	A8XUI8	Protein CBR-BAS-1.	Protein CBR-EGL-46.	0.494
bas-1	sem-4	A8X844	A8XBS8	Protein CBR-BAS-1.	Protein CBR-SEM-4.	0.478
egl-18	sem-4	A8XI58	A8XBS8	Protein CBR-EGL-18.	Protein CBR-SEM-4.	0.504
egl-46	bas-1	A8XUI8	A8X844	Protein CBR-EGL-46.	Protein CBR-BAS-1.	0.494
egl-46	ida-1	A8XUI8	A8X7T6	Protein CBR-EGL-46.	Protein CBR-IDA-1.	0.415
egl-46	lgc-55	A8XUI8	A8XGQ6	Protein CBR-EGL-46.	Protein CBR-LGC-55; Belongs to the ligand-gated ion channel (TC 1.A.9) family.	0.478
egl-46	sem-4	A8XUI8	A8XBS8	Protein CBR-EGL-46.	Protein CBR-SEM-4.	0.640
egl-46	unc-86	A8XUI8	A8XP93	Protein CBR-EGL-46.	POU domain protein.	0.726
flp-19	nlp-3	A8WXQ6	A8WZG8	Protein CBR-FLP-19.	Protein CBR-NLP-3.	0.918
flp-19	unc-86	A8WXQ6	A8XP93	Protein CBR-FLP-19.	POU domain protein.	0.476
ida-1	egl-46	A8X7T6	A8XUI8	Protein CBR-IDA-1.	Protein CBR-EGL-46.	0.415
ida-1	rab-3	A8X7T6	A8WU73	Protein CBR-IDA-1.	Protein CBR-RAB-3.	0.549
lgc-55	egl-46	A8XGQ6	A8XUI8	Protein CBR-LGC-55; Belongs to the ligand-gated ion channel (TC 1.A.9) family.	Protein CBR-EGL-46.	0.478
lgc-55	sem-4	A8XGQ6	A8XBS8	Protein CBR-LGC-55; Belongs to the ligand-gated ion channel (TC 1.A.9) family.	Protein CBR-SEM-4.	0.476
nlg-1	rab-3	A8X4U8	A8WU73	Protein CBR-NLG-1.	Protein CBR-RAB-3.	0.585
nlg-1	unc-40	A8X4U8	A8XKZ7	Protein CBR-NLG-1.	Protein CBR-UNC-40.	0.633
nlp-3	flp-19	A8WZG8	A8WXQ6	Protein CBR-NLP-3.	Protein CBR-FLP-19.	0.918
rab-3	ida-1	A8WU73	A8X7T6	Protein CBR-RAB-3.	Protein CBR-IDA-1.	0.549
rab-3	nlg-1	A8WU73	A8X4U8	Protein CBR-RAB-3.	Protein CBR-NLG-1.	0.585
rab-3	ttx-3	A8WU73	A8WML0	Protein CBR-RAB-3.	Protein CBR-TTX-3.	0.632