PMC:4502369 / 11760-12956 JSONTXT

{"project":"2_test","denotations":[{"id":"25917919-19910308-43377642","span":{"begin":977,"end":981},"obj":"19910308"}],"text":"Novel transcripts detected by the Cufflinks suite were used to identify genetically active, but so far unannotated, regions in the Sus Scrofa genome. Detected sequences that were longer than 130 bp and that had a FPKM value of at least 5 for at least one of the samples were blasted against full genomes in the NCBI database “chromosomes” using the in-house R-package hoardeR (http://cran.r-project.org/web/packages/hoardeR/index.html). Hits that had an identity ratio larger than 0.9 were processed further. Due to the large amount of hits, subsequent analysis focused on hits in the top three species (bos taurus, homo sapiens, and ovis aries). The genome assemblies of the top species used were as follows: Homo sapiens, CRCh38; Bos Taurus, UMD3.1; and Ovis Aries, OAR3.1. Hits were then cross-checked against the gene annotations of the species so that the hits could be grouped into intergenic, intronic, and exonic hits. The R-package edgeR (Robinson, McCarthy and Smyth 2010) function exactTest was then applied for differential expression testing between the oviduct and testis samples and intronic/exonic hits. Values of FDR less than 0.01 were considered to be differentially expressed."}