Computational protocol: CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

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Protocol publication

[…] Using the BioMart Database, the genes within the detected CNVRs were retrieved based on UMD3.1 sequence assembly (http://asia.ensembl.org/biomart/martview/). Ensembl genes overlapping with CNVRs completely or partially were considered as copy number variable and selected for further analysis. To provide insight into the functional enrichment of genes picked out above, we carried out annotation analysis, including GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes), using KOBAS 2.0 [], which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotation. KOBAS 2.0 accepts ID and cross-species sequence similarity mapping and then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). All annotated Ensembl genes are used as background. In addition, we compared CNVRs with the reported cattle QTLs for milk PP and FP traits in the Animal QTL database []. […]

Pipeline specifications

Software tools BioMart, KOBAS
Databases KEGG
Application Genome annotation
Organisms Cucumber necrosis virus, Bos taurus, Homo sapiens