phenobo version 2.1.6
CombineScores is the last node of PheNoBo.
It is the successor of the GeneticNetworkScore node.
This node combines 2 results from the phenotype, metabotype and/or genotype analysis.
The aim of CombineScores is to unite 2 sets of gene scores into a single gene score for each gene. The combined scores are used to rank the genes. Genes with a low rank (appearing first in the list of genes) are likely to cause the patient's condition.
CombineScores requires 2 tables with gene scores. 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.
CombineScores calculates 2 different scores.
Combined Gene Score: The combined gene score is a probability calculated from the scores of 2 different, independent analyses yielding scores g1 and g2. The combined score g is determined by using Bayes' formula: g=g1g2/(g1g2+(1-g1)(1-g2)).
Enrichment score: The probabilities are translated into enrichment scores to facilitate the interpretation of the results. The enrichment score of a gene with probability g is determined as log10(gn) where n denotes the total number of genes. If the enrichment score is greater than 0, the gene score is higher than expected for a random prediction (where all genes get a score of n-1). If the enrichment score is lower than 0, the gene score is lower than expected for a random prediction.
The algorithm of CombineScores is derived from the Phen-Gen tool (see Javed et al., 2014) and is described in more detail at...
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