Research Object Crate for Use Case 11: Related Proteins/Metabolites across DCCs

The workflow starts with selecting RPE as the search term. For the given gene ID (SYMBOL), StringDB PPI was extracted using their API[1]. For the Given StringDB PPI, the list of nodes (Gene Set) is generated. For the Given StringDB PPI, the list of nodes (GeneSet) is generated. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[2]. The gene set was submitted to Enrichr[4]. The gene set was then searched in the Metabolomics Workbench[5] to identify relevant reactions. The gene set was then searched in the Metabolomics Workbench [Metabolomics Workbench, [7] to identify associated metabolites. The gene set was then searched in the Metabolomics Workbench[5] to identify relevant studies related to the genes. 1. Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research vol. 51 D638–D646 (2022). doi:10.1093/nar/gkac1000 2. 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 4. Xie, Z. et al. Gene Set Knowledge Discovery with Enrichr. Current Protocols vol. 1 (2021). doi:10.1002/cpz1.90 5. The Metabolomics Workbench, https://www.metabolomicsworkbench.org/ 7. https://www.metabolomicsworkbench.org/

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