pSI (version 1.1)

candidate.genes: Candidate Gene Lists

Description

This list contains 5 candidate gene lists. They are provided as sample gene lists to be used with fisher.iteration & candidate.overlap functions found in this package.

• candidate.genes$AutDBAutism spectrum disorder candidate gene list from AutDB (N=328)
• candidate.genes$protein.disrupting.rdnvAutism spectrum disorder candidate gene list collected from 4 studies published in 2012 (N = 122)
• candidate.genes$silent.rdnvAutism spectrum disorder negative control gene list collected from 4 studies published in 2012 (N = 122)
• candidate.genes$hcrt.genesNarcolepsy Candidate Gene List (N=63)
• candidate.genes$retinopathy.genesHuman Congenital Retinopathies Disease Gene List (N=120)

NOTE:Supplementary data (human & mouse expression sets, calculated pSI datasets, etc.) can be found in pSI.data package located at the following URL: http://genetics.wustl.edu/jdlab/psi_package/

Format

5 candidate gene lists, each in the form of a character vector, which are contained within one R list.

Source

AutDB Basu SN, Kollu R, Banerjee-Basu S (2009): AutDB: a gene reference resource for autism research. Nucleic Acids Research. 37:D832-D836. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13379 protein.disrupting.rdnv & silent.rdnv Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, et al. (2012): De novo gene disruptions in children on the autistic spectrum. Neuron. 74:285-299. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, et al. (2012): Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 485:242-245. Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, et al. (2012): De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 485:237-241. O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, et al. (2012): Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 485:246-250. hcrt.genes Honda M, Eriksson KS, Zhang S, Tanaka S, Lin L, Salehi A, et al. (2009): IGFBP3 colocalizes with and regulates hypocretin (orexin). PLoS One. 4:e4254. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004254 retinopathy.genes Daiger, SP. RetNet, the Retinal Information Network. https://sph.uth.edu/RetNet/

Details

• candidate.genes$AutDBHand-curated list of Autism Spectrum Disorder (ASD) candidate genes derived from human genetics studies downloaded from AutDB (N=328)
• candidate.genes$protein.disrupting.rdnvList of Protein-Disrupting rare de novo variant affected genes in ASD Probands (N = 122)
• candidate.genes$silent.rdnvList of Silent rare de novo variant affected genes in ASD unaffected siblings (N = 122)
• candidate.genes$hcrt.genesList of differentially dysregulated genes from narcoleptic mice with Hcrt neuron ablation versus control (N=63)
• candidate.genes$retinopathy.genesList of genes identified in human congenital retinopathies downloaded from the curated RetNet database (N=120)

Examples

data(candidate.genes)

names(candidate.genes)

candidate.genes[[5]]