cageminer

The 'cageminer' software tool prioritizes candidate genes by integrating genome-wide association studies (GWAS) with gene coexpression networks. It applies three filtering criteria to identify high-confidence candidates: physical proximity to single nucleotide polymorphisms (SNPs), coexpression with known trait-associated genes, and significant changes in expression levels under specific conditions. The tool allows for scoring and ranking prioritized candidates, aiding in selecting targets for experimental validation.

Topic

GWAS study;Gene expression;Genotype and phenotype;DNA polymorphism;Molecular interactions, pathways and networks

Detail

  • Operation: Gene expression profiling;Gene-set enrichment analysis;Expression correlation analysis

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.8.0

  • Credit: Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil, Conselho Nacional de Desenvolvimento Científico e Tecnológico.

  • Input: -

  • Output: -

  • Contact: Fabrício Almeida-Silva fabricio_almeidasilva@hotmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • cageminer: an R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks
  • Fabricio Almeida-Silva, Thiago M Venancio, cageminer: an R/Bioconductor package to prioritize candidate genes by integrating genome-wide association studies and gene coexpression networks, in silico Plants, Volume 4, Issue 2, 2022, diac018, https://doi.org/10.1093/insilicoplants/diac018
  • https://doi.org/10.1101/2021.08.04.455037
  • PMID: -
  • PMC: -

Download and documentation

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