Torkler, Phillipp and Sauer, Marina and Schwartz, Uwe and Corbacioglu, Selim and Sommer, Gunhild and Heise, Tilman (2024) LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data. NATURE COMMUNICATIONS, 15 (1): 9121. ISSN , 2041-1723
Full text not available from this repository. (Request a copy)Abstract
RNA editing is a highly conserved process. Adenosine deaminase acting on RNA (ADAR) mediated deamination of adenosine (A-to-I editing) is associated with human disease and immune checkpoint control. Functional implications of A-to-I editing are currently of broad interest to academic and industrial research as underscored by the fast-growing number of clinical studies applying base editors as therapeutic tools. Analyzing the dynamics of A-to-I editing, in a biological or therapeutic context, requires the sensitive detection of differential A-to-I editing, a currently unmet need. We introduce the local differential editing index (LoDEI) to detect differential A-to-I editing in RNA-seq datasets using a sliding-window approach coupled with an empirical q value calculation that detects more A-to-I editing sites at the same false-discovery rate compared to existing methods. LoDEI is validated on known and novel datasets revealing that the oncogene MYCN increases and that a specific small non-coding RNA reduces A-to-I editing. Functional implications of A-to-I editing is of broad interest to scientific research. Here, authors introduce the local differential editing index (LoDEI) to detect differential A-to-I editing in RNAseq datasets using a sliding-window approach coupled with an empirical q value calculation.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | IDENTIFICATION; ADAR1; GENE; |
| Subjects: | 500 Science > 570 Life sciences 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Abteilung für Pädiatrische Hämatologie, Onkologie und Stammzelltransplantation Biology, Preclinical Medicine > Institut für Biochemie, Genetik und Mikrobiologie > Lehrstuhl für Biochemie III |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 26 Jan 2026 07:35 |
| Last Modified: | 26 Jan 2026 07:35 |
| URI: | https://pred.uni-regensburg.de/id/eprint/64157 |
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