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dbPSHP specifications

Information


Unique identifier OMICS_08596
Name dbPSHP
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Junwen Wang

Publication for dbPSHP

dbPSHP citations

 (5)
library_books

Ancestors’ dietary patterns and environments could drive positive selection in genes involved in micronutrient metabolism—the case of cofactor transporters

2017
PMCID: 5628472
PMID: 29043008
DOI: 10.1186/s12263-017-0579-x

[…] 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 []. […]

library_books

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome

2017
Mol Biol Evol
PMCID: 5850737
PMID: 28482049
DOI: 10.1093/molbev/msx154

[…] 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 […]

library_books

Exploring genetic associations with ceRNA regulation in the human genome

2017
Nucleic Acids Res
PMCID: 5449616
PMID: 28472449
DOI: 10.1093/nar/gkx331

[…] (,), 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 […]

library_books

In Silico Analysis of Inflammatory Bowel Disease (IBD) GWAS Loci to Novel Connections

2015
PLoS One
PMCID: 4364731
PMID: 25786114
DOI: 10.1371/journal.pone.0119420

[…] 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 […]

library_books

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

2013
Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] 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 […]


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dbPSHP institution(s)
Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China

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