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Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

BMC genomics | 2012

A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation.

Pubmed ID: 23282140 RIS Download

Research resources used in this publication

None found

Antibodies used in this publication

None found

Associated grants

  • Agency: NHGRI NIH HHS, United States
    Id: U01HG004438
  • Agency: NIAAA NIH HHS, United States
    Id: U10AA008401
  • Agency: NIAAA NIH HHS, United States
    Id: P20 AA017828
  • Agency: NIAAA NIH HHS, United States
    Id: U01AA0116667
  • Agency: NIAAA NIH HHS, United States
    Id: R21AA017437
  • Agency: NIAAA NIH HHS, United States
    Id: U01AA016662
  • Agency: NIAAA NIH HHS, United States
    Id: P30AA019372
  • Agency: NIAAA NIH HHS, United States
    Id: P20AA017828
  • Agency: NIAAA NIH HHS, United States
    Id: R01 AA020634
  • Agency: NIAAA NIH HHS, United States
    Id: K02 AA018755
  • Agency: NHGRI NIH HHS, United States
    Id: HHSN268200782096C

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This is a list of tools and resources that we have found mentioned in this publication.


PLINK (tool)

RRID:SCR_001757

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

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Entrez Gene (tool)

RRID:SCR_002473

Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

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International HapMap Project (tool)

RRID:SCR_002846

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

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