Comprehensive SNP Annotation Protocol

The user can create a list of SNP positions and this feature annotates the markers with evidence collected from various other databases and analyses. This list may be significant markers from gene expression or GWAS studies. The annotations can include gene models (RAP (17 (link)), MSUv7 (16 (link)) or FGenesh++ (18 (link))) or promoter regions (FGenesh++, PlantPromDB (24 (link))) if SNPs are located within these loci. The effects of SNP variants were also added using results from SNPEff (25 (link)). For SNPs within gene models, additional evidence about the gene are included using Gene Ontology terms, Plant and Trait Ontology terms and gene names collected from Oryzabase (20 (link)), trait genes from OGRO (21 (link)), and QTL from Q-TARO (26 ), interacting genes from RiceNet v2 (27 (link)) and rice proteins from PRIN (28 (link)). The list of annotations and references are in Supplementary Table S3.

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Mansueto L., Fuentes R.R., Borja F.N., Detras J., Abriol-Santos J.M., Chebotarov D., Sanciangco M., Palis K., Copetti D., Poliakov A., Dubchak I., Solovyev V., Wing R.A., Hamilton R.S., Mauleon R., McNally K.L, & Alexandrov N. (2016). Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Research, 45(Database issue), D1075-D1081.

Publication 2016

Gene markers Genes Gwas studies Plant Prin Proteins Rice Snps Taro

Corresponding Organization : International Rice Research Institute

Other organizations : Ithaca College, Cornell University, University of Arizona, Joint Genome Institute, Lawrence Berkeley National Laboratory

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Protocol cited in 78 other protocols

Variable analysis

independent variables

SNP positions

dependent variables

Evidence collected from various other databases and analyses
Gene models (RAP, MSUv7, or FGenesh++)
Promoter regions (FGenesh++, PlantPromDB)
SNP variant effects (from SNPEff)
Gene Ontology terms
Plant and Trait Ontology terms
Gene names (from Oryzabase)
Trait genes (from OGRO)
QTL (from Q-TARO)
Interacting genes (from RiceNet v2)
Rice proteins (from PRIN)

control variables

Not explicitly mentioned

Annotations

Based on most similar protocols

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