About GeneSetPheno
GeneSetPheno is a user-friendly graphical interface application designed to integrate, summarize, and visualize gene and variant-phenotype associations across gene sets. It integrates data from public databases such as the AstraZeneca PheWAS Portal (https://azphewas.com), FinnGen (https://r11.finngen.fi), GWAS Catalog (https://www.ebi.ac.uk/gwas/), gnomAD (https://gnomad.broadinstitute.org), ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), Human Phenotype Ontology (HPO) (https://hpo.jax.org), and Genotype-Tissue Expression (GTEx) (https://gtexportal.org) to generate visual summaries of gene, genetic variant, phenotype, and association information.
Accessible via:
https://shiny.wehi.edu.au/han.ji/GeneSetPheno/
AstraZeneca PheWAS Portal
Dhindsa RS, Burren OS, Sun BB, Prins BP, Matelska D, Wheeler E, Mitchell J, Oerton E, Hristova VA, Smith KR et al. (2023) Rare variant associations with plasma protein levels in the UK Biobank. Nature. 622(7982):339-347.
Wang Q, Dhindsa RS, Carss K, Harper AR, Nag A, Tachmazidou I, Vitsios D, Deevi SVV, Mackay A, Muthas D et al. (2021) Rare variant contribution to human disease in 281,104 UK Biobank exomes. Nature. 597(7877):527-532.
FinnGen
Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA et al. (2023) FinnGen provides genetic insights from a well-phenotyped isolated population. Nature. 613(7944):508-518.
GWAS catalog
Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J et al. (2023) The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51(D1):D977-d985.
gnomAD
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. (2020) The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 581(7809):434-443.
ClinVar Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42(Database issue):D980-985.
Human Phenotype Ontology (HPO)
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP et al. (2024) The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 52(D1):D1333-d1346.
Genotype-Tissue Expression (GTEx)
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N et al. (2013) The Genotype-Tissue Expression (GTEx) project. Nature Genetics. 45(6):580-585.