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CombineScores2Ports

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...

Input Ports

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Gene Scores 1: a table produced by the GeneticNetworkScore node, e.g. from the phenotype analysis. This node uses the columns gene_id and gene_probability.
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Gene Scores 2: a table produced by the GeneticNetworkScore node, e.g. from the metabotype analysis. This node uses the columns gene_id and gene_probability.

Output Ports

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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 2 independently calculated sets of gene scores (input port 0 and 1). 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.

Installation

To use this node in KNIME, download the below referenced file, save it to your KNIME's plugin folder and restart KNIME.

KNIME 4.3

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Developers

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