| First Author | Bibby JA | Year | 2022 |
| Journal | Cell Rep | Volume | 41 |
| Issue | 8 | Pages | 111697 |
| PubMed ID | 36417885 | Mgi Jnum | J:354541 |
| Mgi Id | MGI:7407991 | Doi | 10.1016/j.celrep.2022.111697 |
| Citation | Bibby JA, et al. (2022) Systematic single-cell pathway analysis to characterize early T cell activation. Cell Rep 41(8):111697 |
| abstractText | 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. |
