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Database Commons - SNPxGE2

SNPxGE2

Citations: 4

z-index 0.43

Short name SNPxGE2
Full name
Description The SNPxGE2 database contains the computationally predicted human SNP-coexpression associations, that is, the differential co-expression between 2 genes is associated with the genotype of an SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 556,873 SNPs and 15,000 gene expression profiles. In order to reduce the computational cost, the SNP-coexpression associations were assessed using gap/substitution scores instead of logistic regression models. The implementation was carried out using 128 Linux cluster nodes in ~30 days and assessed a total of ~1013 SNP-expression-expression combinations. The database can be queried via either gene symbols or reference SNP IDs. For each association, a detailed information page is provided.
URL http://lambchop.ads.uga.edu/snpxge2/index.php
Year founded 2012
Last update & version 2012-02-01    v1.0
Availability Free to all users
University/Institution hosted University of Georgia
Address Athens, GA 30602, USA
City Athens
Province/State GA
Country/Region United States
Contact name Yupeng wang
Contact email wyp1125@gmail.com
Data type(s)
Major organism(s)
Keyword(s)
  • HapMap
  • SNP-coexpression
Publication(s)
  • SNPxGE2: a database for human SNP-coexpression associations. [PMID: 22135417]

    Yupeng Wang, Sandeep J Joseph, Xinyu Liu, Michael Kelley, Romdhane Rekaya
    Bioinformatics (Oxford, England) 2012:28(3)
    4 Citations (Google Scholar as of 2016-02-15)

    Abstract: Recently, gene-coexpression relationships have been found to be often conditional and dynamic. Many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE(2) database contains the computationally predicted human SNP-coexpression associations, i.e. the differential coexpression between two genes is associated with the genotypes of an SNP. These data were generated from a large-scale association study that was based on the HapMap phase I data, which covered 269 individuals from 4 human populations, 556 873 SNPs and 15 000 gene expression profiles. In order to reduce the computational cost, the SNP-coexpression associations were assessed using gap/substitution models, proven to have a comparable power to logistic regression models. The results, at a false discovery rate (FDR) cutoff of 0.1, consisted of 44 769 and 50 792 SNP-coexpression associations based on single and pooled populations, respectively, and can be queried in the SNPxGE(2) database via either gene symbol or reference SNP ID. For each reported association, a detailed information page is provided. http://lambchop.ads.uga.edu/snpxge2/index.php wyp1125@uga.edu, rrekaya@uga.edu.

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200 OK2017-12-29
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200 OK2016-03-09
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200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
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200 OK2016-02-10
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200 OK2016-02-03
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200 OK2016-01-31
200 OK2016-01-29
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200 OK2016-01-18
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200 OK2016-01-15
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200 OK2016-01-10
200 OK2016-01-08
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200 OK2016-01-04

Tags

Expression Phenotype
Homo sapiens
HapMap SNP-coexpression

Record metadata

  • Created on: 2015-06-30
  • Curated by:
    • Lin Xia [2016-03-28]
    • Zhang Zhang [2016-02-15]
Stats