| Previous changeset 9:dd0b4c901d0a (2016-03-23) |
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Commit message:
Uploaded |
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modified:
ProteinInteractions.xml |
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| diff -r dd0b4c901d0a -r c414a56f5874 ProteinInteractions.xml --- a/ProteinInteractions.xml Wed Mar 23 11:15:44 2016 -0400 +++ b/ProteinInteractions.xml Mon Apr 18 10:41:54 2016 -0400 |
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| @@ -39,23 +39,36 @@ </test> </tests> <help> -**Protein Interactions** +SAINT Output to Protein Interaction File +---------------------------------------- -This program will read in a SAINT 'list.txt' file and the interactions from ConsensusPathDB ( http://consensuspathdb.org/ ) and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting protein-protein interactions (PPI's) so that it doesn't affect our SAINT score or include interactions that don't score well. +This tool reads in a *list.txt* file from SAINTexpress and the +interactions from ConsensusPathDB (http://consensuspathdb.org/) and +returns all the known protein-protein interactions observed in the +experiment as a simple interaction file (.SIF). -INPUT + **Note:** This network will not include identified interactions + between baits and preys. This tool queries known interactions + between preys only -SAINT Output: SAINTexpress output. +**1) SAINT Output File** + +SAINTexpress generated *list.txt* file. -SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1). + **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. + "EGFR\_HUMAN" or "P00533"). + +**2) SAINT Score Cutoff** + +SaintScore filter in range 0-1 (default 0.8) -Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1). - * low: no filtering - * medium: >0.5 - * high: >0.7 - * very high: >0.9 +**3) Consensus Path Database Score Cutoff** -Species: Human, Yeast, or Mouse. +Interaction confidence filter in range 0-1 (default 0.8) to specify +which protein interactions in ConsensusPathDB to include. +**4) Species** + +Please specify species. Supported species are Human, Mouse, and Yeast. </help> </tool> \ No newline at end of file |