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a catalog of biological databases

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Database information

SNP@Evolution (a hierarchical database of positive selection on the human genome)

General information

Description: As part of our research scanning for evolutionary signals in HapMap Phase II and Phase III datasets, we built SNP@Evolution as a multi-aspect database focused on positive selection.
Year founded: 2009
Last update: 2009
Version:
Accessibility:
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Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, China
City: beijing
Province/State:
Country/Region: China
Contact name (PI/Team): Changqing Zeng
Contact email (PI/Helpdesk): czeng@genomics.org.cn

Related Database

Record metadata

Created on: 2018-01-27
Curated by:
Dong Zou [2019-12-03]
zhuang xiong [2018-03-24]
zhuang xiong [2018-02-22]

Ranking

All databases:
2665/4692 (43.223%)
Genotype phenotype and variation:
372/635 (41.575%)
2665
Total Rank
20
Citations
1.818
z-index

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Publications

19732458
SNP@Evolution: a hierarchical database of positive selection on the human genome. [PMID: 19732458]
Cheng F, Chen W, Richards E, Deng L, Zeng C.

BACKGROUND: Positive selection is a driving force that has shaped the modern human. Recent developments in high throughput technologies and corresponding statistics tools have made it possible to conduct whole genome surveys at a population scale, and a variety of measurements, such as heterozygosity (HET), FST, and Tajima's D, have been applied to multiple datasets to identify signals of positive selection. However, great effort has been required to combine various types of data from individual sources, and incompatibility among datasets has been a common problem. SNP@Evolution, a new database which integrates multiple datasets, will greatly assist future work in this area.
DESCRIPTION: As part of our research scanning for evolutionary signals in HapMap Phase II and Phase III datasets, we built SNP@Evolution as a multi-aspect database focused on positive selection. Among its many features, SNP@Evolution provides computed FST and HET of all HapMap SNPs, 5+ HapMap SNPs per qualified gene, and all autosome regions detected from whole genome window scanning. In an attempt to capture multiple selection signals across the genome, selection-signal enrichment strength (ES) values of HET, FST, and P-values of iHS of most annotated genes have been calculated and integrated within one frame for users to search for outliers. Genes with significant ES or P-values (with thresholds of 0.95 and 0.05, respectively) have been highlighted in color. Low diversity chromosome regions have been detected by sliding a 100 kb window in a 10 kb step. To allow this information to be easily disseminated, a graphical user interface (GBrowser) was constructed with the Generic Model Organism Database toolkit.
CONCLUSION: Available at http://bighapmap.big.ac.cn, SNP@Evolution is a hierarchical database focused on positive selection of the human genome. Based on HapMap Phase II and III data, SNP@Evolution includes 3,619,226/1,389,498 SNPs with their computed HET and FST, as well as qualified genes of 21,859/21,099 with ES values of HET and FST. In at least one HapMap population group, window scanning for selection signals has resulted in 1,606/10,138 large low HET regions. Among Phase II and III geographical groups, 660 and 464 regions show strong differentiation.

BMC Evol Biol. 2009:9() | 20 Citations (from Europe PMC, 2020-09-19)