Jacob E. Munro, Mark F. Bennett, Melanie Bahlo

PanRank is a method for ranking candidate disease genes based on a known disease gene panel developed by the Bahlo Lab. Rankings are made by a logistic regression model. PanRank is a work in progress and full source code will be made available through GitHub at a later date. Precomputed rankings are available for Genes4Epilepsy and select PanelApp panels.

Implementation

Training Data

Dataset #Gene #Pred. Predictor Description
STRING Coexpression 18,911 18,911 Pairwise gene scores indicating degree of coexpression
STRING Experimental 18,628 18,628 Pairwise gene scores indicating degree of protein-protein interaction
STRING Neighbourhood 4,151 4,151 Pairwise gene scores indicating genomic proximity
STRING Cooccurrence 10,125 10,125 Pairwise gene scores indicating degree of cooccurrence across species
STRING Database 12,927 12,927 Pairwise gene scores indicating interactions across curated databases
GO Biological Process 18,814 8,567 Binary presence of GO Biological Process term annotation
GO Cellular Component 18,814 1,146 Binary presence of GO Cellular Compartment term annotation
GO Molecular Function 18,814 2,027 Binary presence of GO Molecular Function term annotation
GnomAD Constraint 17894 15 “LOEUF” and other gene constraint metrics derived from gnomAD v4
DiSignAtlas 19,003 5,259 Binary presence of gene in differential expressed sets across diseases
PsychENCODE 18,730 1,866 Gene expression in prefrontal cortex across neurodevelopment disorders and controls
DESCARTES 18,529 172 A single cell atlas of foetal gene expression
GeVIR Rank 18,266 15 Gene constraint metrics derived from gnomAD v3
GTEx Expression 18758 54 Median gene expression across 54 postmortem tissues
ZFIN Phenotypes 4,216 21,499 Binary phenotypes in zebrafish matched to human gene orthologs
Homology 19,195 398 Percent identity of human gene homologs across species from Ensembl
Dosage Sensitivity 17,426 2 Prediction scores for gene haplo- and triplo-sensitivity

Results

Precomputed rankings are available for Genes4Epilepsy and select PanelApp panels.