PI: Networking Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level

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Priority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging genetic data to prioritise targets at the gene, pathway and network level. Based on evidence of genetic association from GWAS data, this prioritisation system is able to resolve modulated genes (seed genes) by utilising knowledge of linkage disequilibrium (co-inherited variants), distance from the gene, and evidence of genetic association with gene expression. Seed genes are scored in an integrative way quantifying the genetic influence. Scored seed genes are subsequently used as baits to rank seed genes plus additional (non-seed) genes; this is achieved by iteratively exploring the global connectivity of a gene interaction network. Genes with the top priority are further used to identify/prioritise pathways that are significantly enriched with highly prioritised genes. Prioritised genes are also used to identify a gene network interconnecting many highly prioritised genes but a few lowly prioritised genes as linkers.

Author
Hai Fang, the ULTRA-DD consortium, Julian C Knight
Date of publication
2016-04-25 09:21:46
Maintainer
Hai Fang <hfang@well.ox.ac.uk>
License
GPL-2
Version
1.0.0
URLs

View on R-Forge

Man pages

xPrioritiser
Function to do prioritisation through random walk techniques
xPrioritiserGenes
Function to priorise genes from an input network and the...
xPrioritiserManhattan
Function to visualise prioritised genes using manhattan plot
xPrioritiserPathways
Function to prioritise pathways based on enrichment analysis...
xPrioritiserSNPs
Function to priorise genes given a list of seed SNPs together...
xPrioritiserSubnet
Function to identify a gene network from top prioritised...
xRWR
Function to implement Random Walk with Restart (RWR) on the...

Files in this package

PI/DESCRIPTION
PI/NAMESPACE
PI/R
PI/R/xPrioritiser.r
PI/R/xPrioritiserGenes.r
PI/R/xPrioritiserManhattan.r
PI/R/xPrioritiserPathways.r
PI/R/xPrioritiserSNPs.r
PI/R/xPrioritiserSubnet.r
PI/R/xRWR.r
PI/inst
PI/inst/AS.txt
PI/inst/NEWS
PI/inst/PI.icon.png
PI/inst/PI.logo.png
PI/inst/SLE.txt
PI/inst/Spondyloarthritis.txt
PI/inst/iAnno.txt
PI/inst/xPrioritiser.html
PI/inst/xPrioritiserGenes.html
PI/inst/xPrioritiserManhattan.html
PI/inst/xPrioritiserPathways.html
PI/inst/xPrioritiserSNPs.html
PI/inst/xPrioritiserSubnet.html
PI/inst/xRWR.html
PI/man
PI/man/xPrioritiser.Rd
PI/man/xPrioritiserGenes.Rd
PI/man/xPrioritiserManhattan.Rd
PI/man/xPrioritiserPathways.Rd
PI/man/xPrioritiserSNPs.Rd
PI/man/xPrioritiserSubnet.Rd
PI/man/xRWR.Rd