Research Object Crate for Use Case 1: Explain Drug-Drug Interactions

The workflow starts with selecting Inflammation as the search term. The workflow starts with selecting Penicillin as the search term. The workflow starts with selecting Cortisol as the search term. Gene sets with set labels containing Inflammation were queried from Enrichr[1]. Identified matching terms from the GWAS Catalog 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for GWAS_Catalog_2019. All the identified gene sets were combined using the union set operation. Identified matching terms from the MGI Mammalian Phenotype Level 4 2019[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2019. All the identified gene sets were combined using the union set operation. Identified matching terms from the Human Phenotype Ontology[5] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for Human_Phenotype_Ontology. All the identified gene sets were combined using the union set operation. Gene sets with set labels containing Penicillin were queried from Enrichr[1]. Identified matching terms from the LINCS L1000 Chem Pert Consensus Sigs[6] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for LINCS_L1000_Chem_Pert_Consensus_Sigs. Gene sets with set labels containing Cortisol were queried from Enrichr[1]. Identified matching terms from the LINCS L1000 Chem Pert Consensus Sigs[6] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for LINCS_L1000_Chem_Pert_Consensus_Sigs. The gene sets collected were combined into one gene set library. Multiple GMTs were combined into one GMT. The collection of gene sets was then visualized with a Supervenn diagram Fig.. 1. Xie, Z. et al. Gene Set Knowledge Discovery with Enrichr. Current Protocols vol. 1 (2021). doi:10.1002/cpz1.90 2. Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Research vol. 51 D977–D985 (2022). doi:10.1093/nar/gkac1010 4. Blake, J. A. et al. Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology. Nucleic Acids Research vol. 49 D981–D987 (2020). doi:10.1093/nar/gkaa1083 5. Köhler, S. et al. The Human Phenotype Ontology in 2021. Nucleic Acids Research vol. 49 D1207–D1217 (2020). doi:10.1093/nar/gkaa1043 6. Evangelista, J. E. et al. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research vol. 50 W697–W709 (2022). doi:10.1093/nar/gkac328

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