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  • Oxford University Press (OUP)  (3)
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  • Oxford University Press (OUP)  (3)
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  • 1
    Online Resource
    Online Resource
    BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
    Oxford University Press (OUP) ; 2011
    In:  Nucleic Acids Research Vol. 39, No. suppl_2 ( 2011-07-01), p. W551-W556
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 39, No. suppl_2 ( 2011-07-01), p. W551-W556
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkr312
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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    Online Resource
  • 2
    Online Resource
    Online Resource
    On the impact of batch effect correction in TCGA isomiR expression data
    Oxford University Press (OUP) ; 2021
    In:  NAR Cancer Vol. 3, No. 1 ( 2021-01-06)
    Details
    In: NAR Cancer, Oxford University Press (OUP), Vol. 3, No. 1 ( 2021-01-06)
    Abstract: MicroRNAs (miRNAs) are small non-coding RNAs with diverse functions in post-transcriptional regulation of gene expression. Sequence and length variants of miRNAs are called isomiRs and can exert different functions compared to their canonical counterparts. The Cancer Genome Atlas (TCGA) provides isomiR-level expression data for patients of various cancer entities collected in a multi-center approach over several years. However, the impact of batch effects within individual cohorts has not been systematically investigated and corrected for before. Therefore, the aim of this study was to identify relevant cohort-specific batch variables and generate batch-corrected isomiR expression data for 16 TCGA cohorts. The main batch variables included sequencing platform, plate, sample purity and sequencing depth. Platform bias was related to certain length and sequence features of individual recurrently affected isomiRs. Furthermore, significant downregulation of reported tumor suppressive isomiRs in lung tumor tissue compared to normal samples was only observed after batch correction, highlighting the importance of working with corrected data. Batch-corrected datasets for all cohorts including quality control are provided as supplement. In summary, this study reveals that batch effects present in the TCGA dataset might mask biologically relevant effects and provides a valuable resource for research on isomiRs in cancer (accessible through GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164767).
    Type of Medium: Online Resource
    ISSN: 2632-8674
    URL: Article
    DOI: 10.1093/narcan/zcab007
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 3025038-9
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  • 3
    Online Resource
    Online Resource
    GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis
    Oxford University Press (OUP) ; 2022
    In:  Bioinformatics Vol. 38, No. 7 ( 2022-03-28), p. 2036-2038
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 38, No. 7 ( 2022-03-28), p. 2036-2038
    Abstract: Analysis of focal copy number variations (CNVs) is highly relevant for cancer research, as they pinpoint driver genes. More specifically, due to selective pressure oncogenes and tumor suppressor genes are more often affected by these events than neighboring passengers. In cases where multiple candidates co-reside in a genomic locus, careful comparison is required to either identify multigenic minimally deleted regions of synergistic co-mutations, or the true single driver gene. The study of focal CNVs in large cancer genome cohorts requires specialized visualization and statistical analysis. Results We developed the GenomeTornadoPlot R-package which generates gene-centric visualizations of CNV types, locations and lengths from cohortwise NGS data. Furthermore, the software enables the pairwise comparison of proximate genes to identify co-mutation patterns or driver-passenger hierarchies. The visual examination provided by GenomeTornadoPlot is further supported by adaptable local and global focality scoring. Integrated into the GenomeTornadoPlot R-Package is the comprehensive PCAWG database of CNVs, comprising 2976 cancer genome entities from 46 cohorts of the Pan-cancer Analysis of Whole Genomes project. The GenomeTornadoPlot R-package can be used to perform exploratory or hypothesis-driven analyses on the basis of the PCAWG data or in combination with data provided by the user. Availability and implementation GenomeTornadoPlot is written in R script and released via github: & lt;https://github.com/chenhong-dkfz/GenomeTornadoPlot/ & gt;. The package is under the license of GPL-3.0.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    URL: Article
    DOI: 10.1093/bioinformatics/btac037
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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