dbPSHP

[…] around each SNP was identified and genes annotated using the Bioconductor annotation package TxDb.Hsapiens.UCSC.hg18.knownGene. The comparison of results with literature was done using the data from dbPSHP, a database which contains information about genes and genomic regions from curated publications about positive selection in different human populations []. […]

[…] tions from only one population at a time in order to count the number of sweeps of each type in that population. If a gene found within a sweep window identified by S/HIC was not found in an entry of dbPSHP (), we referred to it as a novel sweep. Visualization of sweep candidates was performed using the UCSC Genome Browser (), along with custom tracks showing values of various population genetic s […]

[…] (,), and grouped the genome-wide association study (GWAS) traits according to ontology mapping (human phenotype ontology and disease ontology) of GWASdb (). We used six statistical measurements from dbPSHP (), including difference of derived allele frequency (DDAF) (), fixation Index (FST) (), Tajima's D (), integrated haplotype score (iHS) (), cross-population extended haplotype homozygosity (XP […]

[…] a as well as other independent studies, many bioinformatics tools have been developed for annotating noncoding variants. In this study, we used four of these publicly available annotation tools, e.g. dbPSHP, CADD, GWAVA and RegulomeDB, for prioritizing IBD associated noncoding variants with potential gene regulatory functions.We analyzed selective constraints on the 152 lead noncoding SNPs (repres […]

[…] tabases (canSAR, DriverDB, FINDBase, HbVar, Lynx, NECTAR, Progenetix) that cover genetic defects leading to various human diseases, including cancer. In addition, three separate databases, Selectome, dbPSHP and 1000 Genomes Selection Browser, report the sites of likely positive selection in human genomes.Model organism databases featured in this issue include regular updates from Saccharomyces Gen […]