{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Muller-Dott S"],"funding":["U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)","Proteogenomics Data Analysis Center","Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)","U.S. Department of Health & Human Services | NIH | National Cancer Institute","NCI NIH HHS","Robert and Janice McNair Foundation","Cancer Prevention and Research Institute of Texas","NIH R35"],"pagination":["4771"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12098709"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(1)"],"pubmed_abstract":["Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active "],"journal":["Nature communications"],"pubmed_title":["Comprehensive evaluation of phosphoproteomic-based kinase activity inference."],"pmcid":["PMC12098709"],"funding_grant_id":["NA","RP220050","R35 CA197588","U24 CA271076","U24 CA271075","U24-CA271076"],"pubmed_authors":["Jaehnig EJ","Johnson JL","Garrido-Rodriguez M","Lussana A","Dugourd A","Saez-Rodriguez J","Savage SR","Yaron-Barir TM","Petsalaki E","Munchic KP","Lei JT","Jiang W","Cantley LC","Mani DR","Krug K","Muller-Dott S","Zhang B"],"additional_accession":[]},"is_claimable":false,"name":"Comprehensive evaluation of phosphoproteomic-based kinase activity inference.","description":"Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active ","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 May","modification":"2026-06-03T07:52:54.681Z","creation":"2026-05-29T03:06:31.33Z"},"accession":"S-EPMC12098709","cross_references":{"pubmed":["40404650"],"doi":["10.1038/s41467-025-59779-y"]}}