Mercurial > repos > bornea > saint_protein_interactions

comparison ProteinInteractions.xml @ 10:c414a56f5874 draft default tip

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author bornea
date Mon, 18 Apr 2016 10:41:54 -0400
parents 830112c59150
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9:dd0b4c901d0a 10:c414a56f5874
37 <param name="input" value="fa_gc_content_input.fa"/> 37 <param name="input" value="fa_gc_content_input.fa"/>
38 <output name="out_file1" file="fa_gc_content_output.txt"/> 38 <output name="out_file1" file="fa_gc_content_output.txt"/>
39 </test> 39 </test>
40 </tests> 40 </tests>
41 <help> 41 <help>
42 **Protein Interactions** 42 SAINT Output to Protein Interaction File
43 ----------------------------------------
43 44
44 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. 45 This tool reads in a *list.txt* file from SAINTexpress and the
46 interactions from ConsensusPathDB (http://consensuspathdb.org/) and
47 returns all the known protein-protein interactions observed in the
48 experiment as a simple interaction file (.SIF).
45 49
46 INPUT 50 **Note:** This network will not include identified interactions
51 between baits and preys. This tool queries known interactions
52 between preys only
47 53
48 SAINT Output: SAINTexpress output. 54 **1) SAINT Output File**
49 55
50 SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1). 56 SAINTexpress generated *list.txt* file.
51 57
52 Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1). 58 **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
53 * low: no filtering 59 "EGFR\_HUMAN" or "P00533").
54 * medium: >0.5
55 * high: >0.7
56 * very high: >0.9
57 60
58 Species: Human, Yeast, or Mouse. 61 **2) SAINT Score Cutoff**
59 62
63 SaintScore filter in range 0-1 (default 0.8)
64
65 **3) Consensus Path Database Score Cutoff**
66
67 Interaction confidence filter in range 0-1 (default 0.8) to specify
68 which protein interactions in ConsensusPathDB to include.
69
70 **4) Species**
71
72 Please specify species. Supported species are Human, Mouse, and Yeast.
60 </help> 73 </help>
61 </tool> 74 </tool>