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Gene_prioritization

Summary Table

NAME CITATION
DEPICT Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H. J., Wood, A. R., Yang, J., ... & Franke, L. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature communications, 6(1), 1-9.
Open Targets Koscielny, G., An, P., Carvalho-Silva, D., Cham, J.A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E. and Pierleoni, A., 2017. Open Targets: a platform for therapeutic target identification and validation. Nucleic acids research, 45(D1), pp.D985-D994.
PoPs Weeks, E. M., Ulirsch, J. C., Cheng, N. Y., Trippe, B. L., Fine, R. S., Miao, J., ... & Finucane, H. K. (2020). Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. medRxiv.
Review-Lappalainen Lappalainen, T., & MacArthur, D. G. (2021). From variant to function in human disease genetics. Science, 373(6562), 1464-1468.
cS2G Lettre, G. (2022). One step closer to linking GWAS SNPs with the right genes. Nature Genetics, 1-2.

DEPICT

  • NAME : DEPICT
  • SHORT NAME : DEPICT
  • FULLNAME : Data-driven Expression Prioritized Integration for Complex Traits
  • DESCRIPTION : an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.
  • URL : https://github.com/perslab/depict
  • CITATION : Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H. J., Wood, A. R., Yang, J., ... & Franke, L. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature communications, 6(1), 1-9.
  • KEY WORDS : co-regulation of gene expression

Open Targets

  • NAME : Open Targets
  • DESCRIPTION : Open Targets is an innovative, large-scale, multi-year, public-private partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation.
  • URL : https://www.opentargets.org/
  • CITATION : Koscielny, G., An, P., Carvalho-Silva, D., Cham, J.A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E. and Pierleoni, A., 2017. Open Targets: a platform for therapeutic target identification and validation. Nucleic acids research, 45(D1), pp.D985-D994.

PoPs

  • NAME : PoPs
  • SHORT NAME : PoPs
  • FULLNAME : gene-level Polygenic Priority Score (PoPS)
  • DESCRIPTION : PoPS is a gene prioritization method that leverages genome-wide signal from GWAS summary statistics and incorporates data from an extensive set of public bulk and single-cell expression datasets, curated biological pathways, and predicted protein-protein interactions.
  • URL : https://github.com/FinucaneLab/pops
  • CITATION : Weeks, E. M., Ulirsch, J. C., Cheng, N. Y., Trippe, B. L., Fine, R. S., Miao, J., ... & Finucane, H. K. (2020). Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. medRxiv.

Review-Lappalainen

  • NAME : Review-Lappalainen
  • CITATION : Lappalainen, T., & MacArthur, D. G. (2021). From variant to function in human disease genetics. Science, 373(6562), 1464-1468.

cS2G

  • NAME : cS2G
  • SHORT NAME : cS2G
  • FULLNAME : optimal combined S2G strategy
  • DESCRIPTION : heritability-based framework for evaluating and combining different S2G strategies to optimize their informativeness for common disease risk
  • URL : https://alkesgroup.broadinstitute.org/cS2G/code
  • CITATION : Lettre, G. (2022). One step closer to linking GWAS SNPs with the right genes. Nature Genetics, 1-2.