PhenoToGeno is part of the phenotype analysis implemented in PheNoBo.
This node is the successor of the Phenomizer node and a predecessor of the NetworkScore node.
The aim of PhenoToGeno is to transform the per-disease results of Phenomizer into predictions of causal genes. The PhenoToGeno algorithm calculates a score for each gene based on the p values reported by Phenomizer. The score of a gene x indicates the probability that x is the causal gene for the patient's disease given the observed symptoms.
PhenoToGeno requires 3 tables with input data: the disease scores, the disease-gene associations and the set of all genes to score. For detailed information about the format of the tables have a look at the example files provided at https://github.com/marie-sophie/mapra.
The algorithm of PhenoToGeno is derived from the Phen-Gen tool (see Javed et al., 2014)...
The PhenoToGeno algorithm is a procedure with 2 main steps.
The first step of the method is a score transformation at disease level. The p value of each disease is converted to the probability that the patient suffers from the disease. A disease with p value p gets a new score s=1/(1+np) where n denotes the total number of diseases.
The second step transfers a disease score to all genes that have an association with that disease. If a disease 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 disease.
The algorithm of PhenoToGeno is derived from the Phen-Gen tool (see Javed et al., 2014) and is described in more detail at...
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