phenobo version 2.1.6
MetaboToGeno is part of the metabotype analysis implemented in PheNoBo.
This node is the successor of the ScoreMetabolites node and a predecessor of the NetworkScore node.
The aim of MetaboToGeno is to transform the per-metabolite results of ScoreMetabolites into predictions of causal genes. The MetaboToGeno algorithm calculates a score for each gene based on the p values reported by ScoreMetabolites. The score of a gene x indicates the probability that x is the causal gene for the patient's metabotype.
MetaboToGeno requires 3 tables with input data: the metabolite scores, the metabolite-gene associations and the set of all genes to score. For detailed information about the format of the tables have a look at the Input Port section and at the example files provided at https://github.com/marie-sophie/mapra.
The MetaboToGeno algorithm is a procedure with 2 main steps.
The first step of the procedure is a score transformation at metabolite level. The p value of each metabolite is converted to the probability that the metabolite is associated with the patient's disease. A metabolite with p value p gets a new score 1/(1+np) where n denotes the total number of metabolites.
The second step transfers a metabolite score to all genes that have an association with that metabolite. If a metabolite does not have any known associations, its score is distributed among all genes. There are several methods (see dialog options) to handle genes that obtain scores from more than one metabolite.
The algorithm of MetaboToGeno is derived from the Phen-Gen tool (see Javed et al., 2014) and is described in more detail at...
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