Matches in SemOpenAlex for { <https://semopenalex.org/work/W4353062956> ?p ?o ?g. }
- W4353062956 abstract "Abstract Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotate them with the Variant Effect Predictor, SpliceAI, and Genotype-Tissue Expression junction counts and compare our results to other tools that integrate genomic and transcriptomic data. While many events are corroborated by the aforementioned tools, the flexibility of RegTools also allows us to identify splice-associated variants in known cancer drivers, such as TP53 , CDKN2A , and B2M , and other genes." @default.
- W4353062956 created "2023-03-23" @default.
- W4353062956 creator A5005950829 @default.
- W4353062956 creator A5017617254 @default.
- W4353062956 creator A5017692700 @default.
- W4353062956 creator A5025443242 @default.
- W4353062956 creator A5026020571 @default.
- W4353062956 creator A5028616783 @default.
- W4353062956 creator A5032085086 @default.
- W4353062956 creator A5035700326 @default.
- W4353062956 creator A5036126324 @default.
- W4353062956 creator A5036890758 @default.
- W4353062956 creator A5041437245 @default.
- W4353062956 creator A5052134884 @default.
- W4353062956 creator A5052449071 @default.
- W4353062956 creator A5054904889 @default.
- W4353062956 creator A5064319129 @default.
- W4353062956 creator A5065644235 @default.
- W4353062956 creator A5068824818 @default.
- W4353062956 creator A5071620573 @default.
- W4353062956 creator A5076166380 @default.
- W4353062956 creator A5078124570 @default.
- W4353062956 creator A5082082558 @default.
- W4353062956 creator A5088846258 @default.
- W4353062956 creator A5089889345 @default.
- W4353062956 creator A5090252960 @default.
- W4353062956 date "2023-03-22" @default.
- W4353062956 modified "2023-10-17" @default.
- W4353062956 title "Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer" @default.
- W4353062956 cites W1547888106 @default.
- W4353062956 cites W1602709607 @default.
- W4353062956 cites W1796435846 @default.
- W4353062956 cites W1846422913 @default.
- W4353062956 cites W1963905877 @default.
- W4353062956 cites W1979014817 @default.
- W4353062956 cites W1988181269 @default.
- W4353062956 cites W2001108463 @default.
- W4353062956 cites W2008350188 @default.
- W4353062956 cites W2018838463 @default.
- W4353062956 cites W2021341670 @default.
- W4353062956 cites W2023648355 @default.
- W4353062956 cites W2034691490 @default.
- W4353062956 cites W2038921819 @default.
- W4353062956 cites W2042012882 @default.
- W4353062956 cites W2043274355 @default.
- W4353062956 cites W2043398720 @default.
- W4353062956 cites W2044433401 @default.
- W4353062956 cites W2057884953 @default.
- W4353062956 cites W2060745559 @default.
- W4353062956 cites W2075661710 @default.
- W4353062956 cites W2088338354 @default.
- W4353062956 cites W2095998476 @default.
- W4353062956 cites W2101214614 @default.
- W4353062956 cites W2102278945 @default.
- W4353062956 cites W2103441770 @default.
- W4353062956 cites W2106332137 @default.
- W4353062956 cites W2108234281 @default.
- W4353062956 cites W2128012941 @default.
- W4353062956 cites W2128323213 @default.
- W4353062956 cites W2132583388 @default.
- W4353062956 cites W2134232737 @default.
- W4353062956 cites W2135166153 @default.
- W4353062956 cites W2136430672 @default.
- W4353062956 cites W2138601221 @default.
- W4353062956 cites W2140729960 @default.
- W4353062956 cites W2142386149 @default.
- W4353062956 cites W2146290346 @default.
- W4353062956 cites W2151794156 @default.
- W4353062956 cites W2152323039 @default.
- W4353062956 cites W2155943701 @default.
- W4353062956 cites W2162946128 @default.
- W4353062956 cites W2169456326 @default.
- W4353062956 cites W2196212938 @default.
- W4353062956 cites W2204287207 @default.
- W4353062956 cites W2267092331 @default.
- W4353062956 cites W2323326409 @default.
- W4353062956 cites W2344561059 @default.
- W4353062956 cites W2346066981 @default.
- W4353062956 cites W2417483443 @default.
- W4353062956 cites W2513185582 @default.
- W4353062956 cites W2605631262 @default.
- W4353062956 cites W2733812791 @default.
- W4353062956 cites W2741482111 @default.
- W4353062956 cites W2750771238 @default.
- W4353062956 cites W2760942750 @default.
- W4353062956 cites W2765417948 @default.
- W4353062956 cites W2774883395 @default.
- W4353062956 cites W2789843538 @default.
- W4353062956 cites W2794804602 @default.
- W4353062956 cites W2795871670 @default.
- W4353062956 cites W2883037081 @default.
- W4353062956 cites W2885227878 @default.
- W4353062956 cites W2888083388 @default.
- W4353062956 cites W2892273485 @default.
- W4353062956 cites W2894573839 @default.
- W4353062956 cites W2901062576 @default.
- W4353062956 cites W2903152738 @default.
- W4353062956 cites W2909194804 @default.
- W4353062956 cites W2944727022 @default.
- W4353062956 cites W2949317881 @default.