GeneticNetworkScore is part of the phenotype and metabotype analysis implemented in PheNoBo.
This node is the successor of the PhenoToGeno node and the MetaboToGeno node.
It is the predecessor of the NetworkScore node.
The aim of GeneticNetworkScore is to refine the gene scores of PhenoToGeno and MetaboToGeno. The node calculates a new score for each gene based on a genetic network. The procedure increases the scores of genes that interact with known causal genes for the patient's condition. Therefore, the GeneticNetworkScore node enables the detection of new disease genes.
GeneticNetworkScore requires 2 tables with input data: the initial gene scores and a genetic network. 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 node implements a random walk with restart on a genetic network. The random walk with restart is an iterative procedure based on the function st+1 = (1-r)Mst + rs0. The function describes a random score transfer along the edges of the network. st is a vector and denotes the scores of all genes after t iterations. The vector s0 contains the initial scores calculated by PhenoToGeno or MetaboToGeno. M is a (sparse) transition matrix representing the edges of the genetic network. The entries mi,j of M give the probability of transferring scores from gene j to gene i. The parameter r gives the fraction of the original scores s0 that is not distributed within the network.
Finally, the gene scores of the random walk with restart are translated into enrichment scores. The enrichment score of a gene with gene score 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.
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to email@example.com, follow @NodePit on Twitter, or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.