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Contents

  • GREP
  • Priority index
  • Open Targets Genetics
  • Drug Targetor
  • Trans-Phar
  • PS4DR
  • Pharmagenic_enrichment_score
  • Reviews&Key_papers

DRUG TARGETOR

  • FULL NAME:DRUG TARGETOR
  • SHORT NAME:DRUG TARGETOR
  • YEAR: 2019
  • DESCRIPTION: This website harnesses results from genome-wide association studies (GWAS), and drug bioactivity data, to prioritize drugs and targets for a given phenotype. Drug Targetor networks are constructed using genetically scored drugs and genes, connected by the type of drug-target or drug-gene interaction
  • URL: https://drugtargetor.com/index_v1.21.html
  • CITATION: Gaspar, H. A., Hübel, C., & Breen, G. (2019). Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes. Bioinformatics, 35(14), 2515-2517.

GREP

  • SHORT NAME: GREP
  • FULL NAME:Genome for REPositioning drugs
  • YEAR: 2019
  • DESCRIPTION: GREP can quantify an enrichment of the user-defined set of genes in the target of clinical indication categories and capture potentially repositionable drugs targeting the gene set. Both can be run in a few seconds!
  • URL: https://github.com/saorisakaue/GREP
  • CITATION: Sakaue, S., & Okada, Y. (2019). GREP: genome for REPositioning drugs. Bioinformatics, 35(19), 3821-3823.

Open Targets Genetics

  • FULL NAME:Open Targets Genetics
  • SHORT NAME:Open Targets Genetics
  • YEAR: 2021
  • DESCRIPTION: Open Targets Genetics is a comprehensive tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets.
  • URL: https://genetics.opentargets.org/
  • CITATION: Ghoussaini, M., Mountjoy, E., Carmona, M., Peat, G., Schmidt, E. M., Hercules, A., ... & Dunham, I. (2021). Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic acids research, 49(D1), D1311-D1320.
  • CITATION:Mountjoy, E., Schmidt, E. M., Carmona, M., Schwartzentruber, J., Peat, G., Miranda, A., ... & Ghoussaini, M. (2021). An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci. Nature Genetics, 53(11), 1527-1533.

Priority index

  • FULL NAME:Priority index
  • SHORT NAME:Priority index
  • YEAR: 2019
  • DESCRIPTION: A Comprehensive Resource for Genetic Targets in Immune-Mediated Disease
  • URL: http://pi.well.ox.ac.uk:3010/
  • CITATION:Fang, H., De Wolf, H., Knezevic, B., Burnham, K. L., Osgood, J., Sanniti, A., ... & Knight, J. C. (2019). A genetics-led approach defines the drug target landscape of 30 immune-related traits. Nature genetics, 51(7), 1082-1091.

Trans-Phar

  • FULL NAME:integration of Transcriptome-wide association study and Pharmacological database
  • SHORT NAME:Trans-Phar
  • YEAR: 2021
  • DESCRIPTION: This software achieves in silico screening of chemical compounds, which have inverse effects in expression profiles compared with genetically regulated gene expression of common diseases, from large-scale pharmacological database (Connectivity Map [CMap] L1000 library).
  • URL: https://github.com/konumat/Trans-Phar
  • CITATION: Konuma, T., Ogawa, K., & Okada, Y. (2021). Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates. Human Molecular Genetics, 30(3-4), 294-304.
  • Hypothesis: "Compounds, which have inverse effects in gene expression profiles when compared with GREx from common diseases, could be detected as potential drug candidates that are effective for disease treatment"

PS4DR

  • FULL NAME:Pathway Signatures for Drug Repositioning
  • SHORT NAME:PS4DR
  • YEAR: 2020
  • DESCRIPTION: This package comprises a modular workflow designed to identify drug repositioning candidates using multi-omics data sets. A schematic figure of the workflow is presented below. The R scripts necessary to run the MSDRP pipeline are located in the R directory.
  • URL: https://github.com/ps4dr/ps4dr
  • CITATION: Emon, M. A., Domingo-Fernández, D., Hoyt, C. T., & Hofmann-Apitius, M. (2020). PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. BMC bioinformatics, 21(1), 1-21.

PES

  • FULL NAME:Pharmagenic_enrichment_score
  • SHORT NAME: PES
  • YEAR: 2020
  • DESCRIPTION: a framework to quantify an individual’s common variant enrichment in clinically actionable systems responsive to existing drugs.
  • CITATION: Reay, W. R., Atkins, J. R., Carr, V. J., Green, M. J., & Cairns, M. J. (2020). Pharmacological enrichment of polygenic risk for precision medicine in complex disorders. Scientific reports, 10(1), 1-12.

Reviews&Key_papers

  • A practical guideline of genomics-driven drug discovery in the era of global biobank meta-analysis
  • YEAR: 2022
  • DESCRIPTION: a practical guideline for genomics-driven drug discovery for cross-population meta-analysis, as lessons from the Global Biobank Meta-analysis Initiative (GBMI)
  • CITATION: Namba, S., Konuma, T., Wu, K. H., Zhou, W., Okada, Y., & Global Biobank Meta-analysis Initiative. (2022). A practical guideline of genomics-driven drug discovery in the era of global biobank meta-analysis. Cell Genomics, 2(10), 100190.