CombineScores is the last node of PheNoBo.
It is the successor of the GeneticNetworkScore node.
This node combines the results of the phenotype, metabotype and genotype analysis.
The aim of CombineScores is to unite the gene scores of the phenotype, metabotype and genotype analysis 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 3 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 3 different, independent analyses
yielding scores g1, g2 and g3.
The combined score g is determined by using Bayes' formula:
g=g1g2g3/(g1g2g3+(1-g1)(1-g2)(1-g3)).
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...
Input Ports
- Gene Scores 1 (Phenotype analysis): a table produced by the GeneticNetworkScore node. This node uses the columns gene_id and gene_probability.
- Gene Scores 2 (Metabotype analysis): a table produced by the GeneticNetworkScore node. This node uses the columns gene_id and gene_probability.
- Gene Scores 3 (Genotype analysis): a table produced by the GeneticNetworkScore node. This node uses the columns gene_id and gene_probability.
Output Ports
- Combined Scores: Each row represents a gene and consists of 3 columns: gene_id, gene_probability and enrichment_score. The column gene_probability contains the combined gene scores based on 3 independently calculated sets of gene scores (input port 0,1 and 2). The gene probability indicates the likelihood that the gene is causal for the patient's disease. The column enrichment_score is a gene score that is normalized for the total number of genes. If the enrichment score is above 0, the gene probability is higher than expected for a random prediction.
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