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    flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data

    Cite as: Szkop, Krzysztof J. and Moss, David S. and Nobeli, Irene (2019): flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Birkbeck College, University of London. doi: https://doi.org/10.18743/DATA.00035

    Description

    An “idealized” dataset of RNA-seq reads was created using the polyester R package (Frazee et al., 2015). This simulated dataset is clean of technical biases and fold changes between isoforms are known, allowing testing of the sensitivity limits of the method in the absence of external factors. The simulation experiment comprises 20 samples, 10 in each of two conditions.
    For the "main" dataset, polyadenylation sites splitting each transcript into two isoforms (short and long) were obtained from the poly(A) site atlas (Gruber et al., 2016) for 11000 human transcripts. Each isoform (“short” and “short + long”) was simulated as a different transcript. The expression of the “shot + long” isoform was unchanged between conditions, whereas eleven different fold changes were applied between conditions for the “short” isoform in order to produce a range of different ratios, R. Hence, each fold change is represented by ~ 1000 transcripts in the dataset. Additionally, for each fold change category we assigned 100 different mean expression levels (from 100 to 1000) with the aim of sampling the effect of the expression level on the ability of the method to detect alternative polyadenylation events.
    For the "biased" dataset, the aim was to create a scenario where fold changes between two conditions are confounded by the presence of an additional factor. In the specific example set up, we created an imbalanced dataset with 1000 transcripts where male and female-origin samples are present in unequal numbers in the control (7 males and 3 females) and condition (3 males and 7 females) groups. Although the group membership for the factor of interest (condition) plays no role in the choice of polyadenylation site of these transcripts, membership to male or female group does, confounding the outcome of methods that do not take into account additional covariates.

    Collection Method

    Simulated RNA-seq data using polyester package (Frazee et al., 2015)

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    Additional Metadata

    Data

    Metadata

    Dataset Title:

    flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data
    Creators:

    Szkop, Krzysztof J. and Moss, David S. and Nobeli, Irene
    School/Department:

    Birkbeck Schools and Research Centres > School of Science > Biological Sciences
    Data collection method:

    Simulated RNA-seq data using polyester package (Frazee et al., 2015)
    Statement on legal, ethical, and access issues:

    Not applicable
    Depositing User: Krzysztof Szkop
    Date Deposited: 24 Jan 2019 10:47
    Last Modified: 01 Jul 2022 16:01
    Publisher: Birkbeck College, University of London

    Export / Share Citation

    Cite as: Szkop, Krzysztof J. and Moss, David S. and Nobeli, Irene (2019): flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Birkbeck College, University of London. doi: https://doi.org/10.18743/DATA.00035

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