Mercurial > repos > bornea > saint_bubblebeam

comparison Bubblebeam_For_SAINT_wrapper.xml @ 28:24d4f1350c83 draft

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author bornea
date Fri, 29 Jan 2016 09:37:09 -0500
parents 64b822045467
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27:ab9ace68e3b5 28:24d4f1350c83
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59 OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome 59 OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome
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61 Bubble graphs are generated for each bait where: 61 Bubble graphs are generated for each bait where:
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63 * x axis is the natural log of the NSAF values 63 * x axis is the natural log of the NSAF values
64 * y axis is the observed log2 fold change (as compared to control) 64 * y axis is the observed log2 fold change (as compared to control)
65 * bubble radius is proportional to the average observed spectra 65 * bubble radius is proportional to the average observed spectra
66 66
67 OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan 67 OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan
68 68
69 APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option. 69 APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option.
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111 Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database 111 Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database
112 112
113 Suggestions: 113 Suggestions:
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115 * low: 0 115 * low: 0
116 * medium: 0.5 116 * medium: 0.5
117 * high: 0.7 117 * high: 0.7
118 * very high: 0.9 118 * very high: 0.9
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120 List of Uniprot IDs to Include: 120 List of Uniprot IDs to Include:
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122 Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam. 122 Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam.
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