{"doi":"10.1016/j.celrep.2022.111697","title":"Systematic single-cell pathway analysis to characterize early T cell activation","abstract":"Pathway analysis is a key analytical stage in the interpretation of omics data, providing a powerful method for detecting alterations in cellular processes. We recently developed a sensitive and distribution-free statistical framework for multisample distribution testing, which we implement here in the open-source R package single-cell pathway analysis (SCPA). We demonstrate the effectiveness of SCPA over commonly used methods, generate a scRNA-seq T cell dataset, and characterize pathway activity over early cellular activation. This reveals regulatory pathways in T cells, including an intrinsic type I interferon system regulating T cell survival and a reliance on arachidonic acid metabolism throughout T cell activation. A systems-level characterization of pathway activity in T cells across multiple tissues also identifies alpha-defensin expression as a hallmark of bone-marrow-derived T cells. Overall, this work provides a widely applicable tool for single-cell pathway analysis and highlights regulatory mechanisms of T cells.","journal":"Cell Reports","year":2022,"id":232889,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":158,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9511,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":275490,"name":"Divyansh Agarwal","orcid":"0000-0003-0404-6877","position":1,"is_corresponding":false},{"id":278218,"name":"Tilo Freiwald","orcid":"0000-0002-4759-717X","position":2,"is_corresponding":false},{"id":278216,"name":"Natalia Kunz","orcid":"0000-0001-6583-360X","position":3,"is_corresponding":false},{"id":486214,"name":"Nicolas S. Merle","orcid":"0000-0003-0379-7724","position":4,"is_corresponding":false},{"id":278215,"name":"Erin E. West","orcid":"0000-0002-7103-8394","position":5,"is_corresponding":false},{"id":486215,"name":"Parul Singh","orcid":"0000-0002-2626-064X","position":6,"is_corresponding":false},{"id":340208,"name":"André Larochelle","orcid":"0000-0003-0685-2186","position":7,"is_corresponding":false},{"id":845316,"name":"Fariba Chinian","orcid":null,"position":8,"is_corresponding":false},{"id":844312,"name":"Somabha Mukherjee","orcid":"0000-0001-6772-3404","position":9,"is_corresponding":false},{"id":278231,"name":"Behdad Afzali","orcid":"0000-0003-2968-1156","position":10,"is_corresponding":false},{"id":254219,"name":"Claudia Kemper","orcid":"0000-0003-4196-1417","position":11,"is_corresponding":false},{"id":17026,"name":"Nancy R. Zhang","orcid":"0000-0002-0880-5749","position":12,"is_corresponding":false},{"id":385263,"name":"Jack Bibby","orcid":"0000-0002-0875-446X","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":null,"created_at":"2026-07-19T00:21:18.683916Z","pmid":"36417885","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}