Journal Article

DKFZ-2022-03214

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Revana: a comprehensive tool for regulatory variant analysis and visualization of cancer genomes.

Ulrich, E. (First author)DKFZ* ; Pfister, S. M.DKFZ* ; Jäger, N. (Last author)DKFZ*

2023
Oxford Univ. Press Oxford

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Please use a persistent id in citations: doi:10.1093/bioinformatics/btac831

Abstract: As non-coding driver mutations move more into the focus of cancer research, a comprehensive and easy to use software solution for regulatory variant analysis and data visualization is highly relevant. The interpretation of regulatory variants in large tumor genome cohorts requires specialized analysis and visualization of multiple layers of data, including for example breakpoints of structural variants, enhancer elements and additional available gene locus annotation, in the context of changes in gene expression.We introduce a user-friendly tool, Revana (REgulatory Variant ANAlysis), that can aggregate and visually represent regulatory variants from cancer genomes in a gene-centric manner. It requires whole genome (WGS) and RNA sequencing (RNA-Seq) data of a cohort of tumor samples and creates interactive HTML reports summarizing the most important regulatory events.Revana is implemented in R and JavaScript. It is available for download as an R package under <https://github.com/KiTZ-Heidelberg/revana>. Sample results can be viewed under <https://github.com/KiTZ-Heidelberg/revana-demo-report> and a short walkthrough is available under <https://github.com/KiTZ-Heidelberg/revana-demo-data>.Supplementary data are available at Bioinformatics online.

Note: #EA:B062#LA:B062# / 2023 Jan 1;39(1):btac831

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Contributing Institute(s):

1. B062 Pädiatrische Neuroonkologie (B062)
2. DKTK HD zentral (HD01)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2022

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Database coverage:
; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DOAJ Seal ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 5 ; JCR ; Nationallizenz ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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