Candidate Gene Lists

Five candidate gene lists, provided as examples for use with fisher.iteration and candidate.overlap.

Usage

candidate.genes

Format

A list of five character vectors of official gene symbols:

AutDB

Hand-curated list of Autism Spectrum Disorder (ASD) candidate genes derived from human genetics studies, downloaded from AutDB (N = 328).

protein.disrupting.rdnv

Genes affected by protein-disrupting rare de novo variants in ASD probands, collected from four exome studies published in 2012 (N = 122).

silent.rdnv

Negative control: genes affected by silent rare de novo variants in unaffected siblings, from the same four studies (N = 122).

hcrt.genes

Genes differentially regulated in narcoleptic mice with hypocretin (Hcrt) neuron ablation versus controls (N = 63).

retinopathy.genes

Genes implicated in human congenital retinopathies, from the curated RetNet database (N = 120).

Source

AutDB: Basu SN, Kollu R, Banerjee-Basu S (2009). AutDB: a gene reference resource for autism research. Nucleic Acids Research 37:D832-D836. doi:10.1093/nar/gkn835

protein.disrupting.rdnv and silent.rdnv: Iossifov I, Ronemus M, Levy D, et al. (2012). De novo gene disruptions in children on the autistic spectrum. Neuron 74:285-299. doi:10.1016/j.neuron.2012.04.009 . Neale BM, Kou Y, Liu L, et al. (2012). Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485:242-245. doi:10.1038/nature11011 . Sanders SJ, Murtha MT, Gupta AR, et al. (2012). De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485:237-241. doi:10.1038/nature10945 . O'Roak BJ, Vives L, Girirajan S, et al. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485:246-250. doi:10.1038/nature10989 .

hcrt.genes: Honda M, Eriksson KS, Zhang S, et al. (2009). IGFBP3 colocalizes with and regulates hypocretin (orexin). PLoS ONE 4:e4254. doi:10.1371/journal.pone.0004254

retinopathy.genes: Daiger SP. RetNet, the Retinal Information Network. https://web.sph.uth.edu/RetNet/

Examples

data(candidate.genes)
names(candidate.genes)
#> [1] "AutDB"                   "protein.disrupting.rdnv"
#> [3] "silent.rdnv"             "hcrt.genes"             
#> [5] "retinopathy.genes"      
lengths(candidate.genes)
#>                   AutDB protein.disrupting.rdnv             silent.rdnv 
#>                     328                     122                     122 
#>              hcrt.genes       retinopathy.genes 
#>                      63                     120 
head(candidate.genes$AutDB)
#> [1] "ABAT"    "ADA"     "ADK"     "ADORA2A" "ADRB2"   "ADSL"