(5 nodes) PAP2 superfamily C-terminal network (Caenorhabditis briggsae)

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Experiments

Co-purification, co-crystallization, Yeast2Hybrid, Genetic Interactions, etc ... as imported from primary sources.

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Neighborhood

Groups of genes that are frequently observed in each other's genomic neighborhood.

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Textmining

Automated, unsupervised textmining - searching for proteins that are frequently mentioned together.

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Fusion

Genes that are sometimes fused into single open reading frames.

STRING allows inspection of the interaction evidence for any given network. Choose any of the viewers above (disabled if not applicable in your network).

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:
	sms-2	Protein CBR-SMS-2. (336 aa)
	sms-5	Protein CBG07059. (328 aa)
	CBG14086	Protein CBG14086. (493 aa)
	sms-3	Protein CBR-SMS-3. (297 aa)
	sms-1	Protein CBR-SMS-1. (407 aa)

Your Current Organism:

Caenorhabditis briggsae

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

Basic Settings

Network type:

full STRING network

( the edges indicate both functional and physical protein associations )

physical subnetwork

( the edges indicate that the proteins are part of a physical complex )

meaning of network edges:

evidence

( line color indicates the type of interaction evidence )

confidence

( line thickness indicates the strength of data support )

active interaction sources:

Textmining

Experiments

Databases

Co‑expression

Neighborhood

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Co‑occurrence

minimum required interaction score:

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Advanced Settings

network display mode:

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( network is a simple bitmap image; not interactive )

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( network is a scalable vector graphic [SVG]; interactive )

network display options:

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Export your current network:

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file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

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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

... as short tabular text output:

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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
sms-1	sms-2	A8X0T5	A8X5S1	Protein CBR-SMS-1.	Protein CBR-SMS-2.	0.910
sms-1	sms-3	A8X0T5	A8XDY1	Protein CBR-SMS-1.	Protein CBR-SMS-3.	0.916
sms-2	sms-1	A8X5S1	A8X0T5	Protein CBR-SMS-2.	Protein CBR-SMS-1.	0.910
sms-2	sms-3	A8X5S1	A8XDY1	Protein CBR-SMS-2.	Protein CBR-SMS-3.	0.908
sms-3	sms-1	A8XDY1	A8X0T5	Protein CBR-SMS-3.	Protein CBR-SMS-1.	0.916
sms-3	sms-2	A8XDY1	A8X5S1	Protein CBR-SMS-3.	Protein CBR-SMS-2.	0.908

[ The below analysis is limited to the network nodes included in the specified statistical background ]

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Clustering Options

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( legacy version of k-means algorithm )

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EMBL - European Molecular Biology Laboratory

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