candidate.genes: Candidate Gene Lists

In pSI: Specificity Index Statistic

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$AutDB
  Autism spectrum disorder candidate gene list from AutDB (N=328)

• candidate.genes$protein.disrupting.rdnv
  Autism spectrum disorder candidate gene list collected from 4 studies published in 2012 (N = 122)

• candidate.genes$silent.rdnv
  Autism spectrum disorder negative control gene list collected from 4 studies published in 2012 (N = 122)

• candidate.genes$hcrt.genes
  Narcolepsy Candidate Gene List (N=63)

• candidate.genes$retinopathy.genes
  Human 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.

Details

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

• candidate.genes$protein.disrupting.rdnv
  List of Protein-Disrupting rare de novo variant affected genes in ASD Probands (N = 122)

• candidate.genes$silent.rdnv
  List of Silent rare de novo variant affected genes in ASD unaffected siblings (N = 122)

• candidate.genes$hcrt.genes
  List of differentially dysregulated genes from narcoleptic mice with Hcrt neuron ablation versus control (N=63)

• candidate.genes$retinopathy.genes
  List of genes identified in human congenital retinopathies downloaded 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. 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/

Examples

data(candidate.genes)

names(candidate.genes)

candidate.genes[[5]]

Example output

Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata: 
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata: 
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

[1] "AutDB"                   "protein.disrupting.rdnv"
[3] "silent.rdnv"             "hcrt.genes"             
[5] "retinopathy.genes"      
  [1] "BBS4"     "SPATA7"   "TOPORS"   "GUCA1B"   "GPR98"    "PDE6C"   
  [7] "ABCA4"    "AIPL1"    "ADAM9"    "PCDH15"   "OPN1SW"   "CDH3"    
 [13] "CFH"      "CHM"      "CLN3"     "CNGA1"    "COL11A1"  "COL2A1"  
 [19] "COL9A1"   "CRX"      "VCAN"     "DMD"      "FZD4"     "OPN1MW"  
 [25] "GNAT1"    "GNAT2"    "GUCA1A"   "INVS"     "JAG1"     "PHYH"    
 [31] "LRP5"     "IDH3B"    "CRB1"     "MERTK"    "MTTP"     "MYO7A"   
 [37] "NRL"      "OAT"      "OTX2"     "PDE6B"    "PDE6G"    "PEX7"    
 [43] "PROM1"    "PRPH2"    "PRPF8"    "RB1"      "RBP3"     "RBP4"    
 [49] "RDH5"     "RGS9"     "RLBP1"    "ROM1"     "RPE65"    "RPGR"    
 [55] "RS1"      "SAG"      "SEMA4A"   "RHO"      "EFEMP1"   "TEAD1"   
 [61] "TIMP3"    "TREX1"    "TULP1"    "UNC119"   "USH2A"    "CDH23"   
 [67] "WFS1"     "PDE6A"    "CLRN1"    "CC2D2A"   "NYX"      "OFD1"    
 [73] "FSCN2"    "IMPDH1"   "NR2E3"    "GRK1"     "KCNV2"    "BBS12"   
 [79] "RGS9BP"   "ATXN7"    "NPHP4"    "TSPAN12"  "ABCC6"    "CNGB3"   
 [85] "CACNA2D4" "BBS9"     "IQCB1"    "PITPNM3"  "OPA3"     "TTPA"    
 [91] "KLHL7"    "AHI1"     "NPHP1"    "CACNA1F"  "RP9"      "ARL6"    
 [97] "RGR"      "MKKS"     "INPP5E"   "TMEM126A" "BBS2"     "PRPF31"  
[103] "TRIM32"   "PRPF3"    "PEX1"     "BBS7"     "BBS10"    "USH1C"   
[109] "BBS5"     "CABP4"    "OPA1"     "PANK2"    "LCA5"     "TTC8"    
[115] "SDCCAG8"  "RPGRIP1"  "RDH12"    "LRAT"     "ELOVL4"   "CNNM4"   

pSI documentation built on May 1, 2019, 10:28 p.m.