#acl All:read

= SH3 Interactome Conserves General Function Over Specific Form =

This data is supplementary material for:

''SH3 Interactome Conserves General Function Over Specific Form''

== Data ==

 * Phage display peptide data in brain format (see below)
   * [[attachment:WormSH3.zip]]
 * Protein-protein interaction data in PSI-MI 2.5 format
   * [[attachment:WormSH3PPIs.zip]]
   * Protein-protein interaction data has been submitted to the [[http://www.ebi.ac.uk/intact/|IntAct database]].

== File Format ==
Each zip file contains a set of ''peptide files'' as shown in the example below. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique. These files can be directly loaded into the [[http://www.baderlab.org/Software/LOLA|LOLA software]], which can be used to visualize peptide sets as sequence logos and to create Logo Trees, or the [[http://baderlab.org/Software/BRAIN|BRAIN software]], which is a Cytoscape plugin that can be used to search protein sequence databases for proteins that contain sequence patterns matching a set of peptides.

The peptide file consists of a '''Header Section''' that describes the protein and domain sequence, and a '''Peptide Section''' that lists and describes the peptide ligands.

The peptides have been aligned with MUSCLE (Nucl. Acids Res. (2004) 32 (5): 1792-1797) and all multiple alignments have been manually curated. For some domains (STAM-1 = C34G6.7 and HUM-1 = F29D10.4), the interacting peptides have bee split into two groups corresponding to Class I (RxxPxxP) and class II (PxxPxR) SH3 ligands.

Example:
{{{
Gene Name	B0303.7
Accession	Refseq:B0303.7
Organism	C. elegans
NCBITaxonomy	ID9606
Domain Number	1
Domain Type	SH3
Interpro ID	IPR001452
Technique	Phage Display High Valency
Domain sequence	PSYSAPAISTPYGIAKFDYAPTQSDEMGLRIGDTVLISKKVDAEWFYGENQNQRTFGIVPSSYLDIKIPLKEAFTAL
PeptideName	Peptide	CloneFrequency
1	GSEVPPVPPRPV	1
2	SLDPPPVPPRPV	1
3	ASARPPVPPRPL	1
4	SNLDHWQPGEPV	1
5	DMRAPPVPPRPD	1
6	XXXAPLPPPRPD	1
7	FQDVRIAPQVPA	1
8	APVAPEPPPRPH	1
9	SXIVPTVPPVPD	1
10	GQTAPPVPARPA	1
11	EGVAPPPPPRPV	1
12	FTTAPPVPPRPL	1
13	LGTAPPVPARPI	1
14	SEILPTIPPRPD	1
15	SGTPPPVPTRPD	1
16	VTEAPQVPPRPF	1
17	GETAPPVPPRPL	1
18	LPEPPPPPPRPV	1
19	LLDTPAVPTRPC	1
20	YGAAPPVPPRPV	1
21	QPKAPPVPVRPS	1
22	LLDTPAVPTRPC	1
23	GEYAPPVPPRPD	1
24	DITAPPPPPRPY	1
25	VRETPPVPARPA	1
26	SLDPPPVPPRPV	1
27	LDRVPPPPARPS	1
28	XGEAPPAPPRPG	1
29	VDAAPPVPQRPA	1
30	GATAPPVPPRPN	1
31	GDLPPPVPPRPS	1
}}}

==== Header Section ====

Describes the protein, domain, and experiment. Required fields are indicated with a '''*'''.

'''NOTE:''' This section is in a 2 column format. Field names must be separated from their values with a single TAB character. Multiple TABs, or spaces, are not accepted.

 '''Gene Name:*''' An identifier that represents the gene or protein sequence. Not required to be unique.

 '''Accession:*''' A space-separated list of database accession identifiers for the protein or corresponding gene.

 '''Organism:''' Description of taxon of the protein.

 '''NCBITaxonomyID*:''' Taxon identifier from NCBI's Taxonomy repository.

 '''Domain Number*:''' A number that represents the position of the domain sequence within the protein. For proteins containing multiple instances of the domain, this number helps distinguish the position of these instances. Set to "0" if instance information is not known.

 '''Domain Type:*''' The formal name of the domain, e.g. WW, PDZ, SH3.

 '''Interpro ID:''' The Interpro database identifier for the domain.

 '''Technique:''' The experimental method used to identify potential ligands of the protein.

 '''Domain Sequence:*''' The amino-acid sequence of the domain region.

 '''Domain Range:''' The amino-acid position range for the domain region within the protein.

 '''Comment:''' Notes, additional information, personal comments pertaining to this file.

==== Peptide Section ====

Describes the experimentally determined peptide ligands. The peptide sequences must be in '''multiple alignment format'''. The sequences should contain '''no gaps''', and should be padded with the '''X''' symbol on both sides, where required, such that all sequences have identical length.

'''NOTE:''' This section is in a 5-column format. Column headers and values must be separated with a single TAB character. Multiple TABs or spaces are not accepted.

Required fields are indicated with a '''*'''.

 '''!PeptideName:*''' A ''unique'' numerical symbol assigned to each peptide ligand. To omit a peptide, set to a non-numeric value (e.g. "A"). '''Values in this column must be unique.'''

 '''Peptide:*''' The peptide ligand sequence.

 '''!CloneFrequency:''' Applies only to phage display data: the observed frequency of the peptide in the cloning step.

 '''!QuantData:''' A number that relatively or absolutely quantifies the protein-ligand interaction. E.g. The optical density (OD) from a protein chip experiment.

 '''!ExternalIdentifier:''' A database identifier for the peptide.