The Human Gene Population Genetic Difference database
The Human Gene Population Genetic Difference database
HGPGD:The Human Gene Population Genetic Difference database
Citation:
Jiang Y, Zhang R, Lv H, Li J, Wang M, et al. (2013) HGPGD: The Human Gene Population Genetic Difference Database. PLoS ONE 8(5): e64150.
doi:10.1371/journal.pone.0064150
Introduction:
Human populations live in variable environments, and many layers of demographic and evolutionary events, such as migrations, population expansions, colonizations, genetic drift, selection, recombination and mutation, have shaped human genetic variation.
Different functional genes or functional pathways (genes are not independent to each other, a group of genes often act together to perform some specific biological tasks) would display different degree of genetic diversity or evolutionary conservatism among recent human population splits.
HGPGD provides search of population genetic differences from single gene-level and system-level. User can search the population genetic differences of single gene, KEGG pathway and GO category:
1. Search genetic difference of single gene
Enter a gene list and select a population genetic feature, user can obtain the genetic differences of the gene among 11 HapMap sample populations. There are total 18,158 single genes in HGPGD. These genes have at least 2 SNPs in the gene region.
2. Search genetic difference of KEGG pathway
Enter a KEGG pathway list and select a population genetic feature, user can obtain the genetic differences of the pathway among 11 HapMap sample populations. There are total 220 KEGG pathways in HGPGD. These pathways have at least 10 genes.
3. Search genetic difference of GO category
Enter a GO term list and select a population genetic feature, user can obtain the genetic differences of the GO category among 11 HapMap sample populations. There are total 4,989 GO categories in HGPGD. These categories have at least 10 genes.
Note:
(1)For each functional gene, functional pathway or GO category, user can search the population differences in three mainly genetic aspects: allele frequency (maf and Fst), linkage disequilibrium (LD) pattern (six indicators: r^2, Dprime, Block number, Block size, SNP density and Haplotype diversity), and transferability of tagSNPs (three indicators: tagSNP percent, captured percent and average max r^2) between pair wise HapMap sample populations (total 11 HapMap sample populations, 55 population pairs).
(2) Here, populations refer to HapMap populations. At present, there are 11 HapMap sample populations. User can search genetic differences between each pairwise populations (total 55 pair populations).
Population name abbreviations (11 HapMap sample populations):
ASW:African Americans from the American Southwest
CEU:Utah residents with Northern and Western European ancestry from the CEPH collection
CHB:Han Chinese in Beijing, China
CHD:Chinese in Metropolitan Denver, Colorado
GIH:Gujarati Indians in Houston, Texas
JPT:Japanese in Tokyo, Japan
LWK:Luhya in Webuye, Kenya
MEX:Mexican ancestry in Los Angeles, California
MKK:Maasai in Kinyawa, Kenya
TSI:Toscans in Italy
YRI:Yoruba in Ibadan, Nigeria
We hope that when the researchers performed gene based, pathway based or GO category based research, they can take full account of the genetic differences between populations.
Here,you can search the population genetic differences of single gene, KEGG pathway and GO category.
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