snpGeneSets: An R Package for Genome-Wide Study Annotation.
Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/.
Department of Data Science, University of Mississippi Medical Center, Jackson, Mississippi 39216 hmei@umc.edu arrow64@163.com.|Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai Shi, China, 200023.
Hao
H
Mei
Department of Biology, Tougaloo College, Jackson, Mississippi.
Lianna
L
Li
Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai Shi, China, 200023.
Fan
F
Jiang
Department of Data Science, University of Mississippi Medical Center, Jackson, Mississippi 39216.
Jeannette
J
Simino
Department of Data Science, University of Mississippi Medical Center, Jackson, Mississippi 39216.
Michael
M
Griswold
Department of Neurology, University of Mississippi Medical Center, Jackson, Mississippi 39174.
Thomas
T
Mosley
Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai Shi, China, 200023 hmei@umc.edu arrow64@163.com.
Shijian
S
Liu
D018388:Codon, Terminator; D019295:Computational Biology / Q000379:methods*; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012984:Software; D024363:Transcription Initiation Site; D064878:Web Browser
D018388:Codon, Terminator
SNP; gene; gene set; genetic annotation