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3 results for “APARENT2”
APARENT2 Genome-wide In-silico Saturation Mutagenesis
<p>In-silico saturation mutagenesis predictions for all polyadenylation signals found in PolyADB V3 using the APARENT2 model (transcript-wide). The file 'aparent2_ism_scores_polyadb_v3.csv.gz' contains all data. The file 'aparent2_ism_scores_polyadb_v3_cutoff.csv.gz' contains only variants with more than 1.25-fold increase or decrease in isoform odds. The data columns 'delta_logodds' and 'delta_usage' contain variant isoform log odds ratios and isoform proportion differences (wrt. PolyADB measurements) for polyadenylation occurring anywhere +/- 100bp of the canonical cleavage site. The columns 'delta_logodds_narrow' and 'delta_usage_narrow' contains log odds ratios and proportion differences for cleaveage that occurs +0bp to +50bp immediately downstream of the canonical core hexamer motif. The data columns 'pas_position_hg19' and 'pas_position_hg38' indicate the start coordinate of the core hexamer.</p>
APARENT2 Training Data and Models
<p>Processed training data for the APARENT2 model (measurements from the random MPRA and designed oligo pool originally published by Bogard et al., 2019; see https://doi.org/10.1016/j.cell.2019.04.046 for reference). This repository also contains the APARENT2 model file. For more information on the training procedure, see the <em>Genome Biology</em> article "Deciphering the impact of genetic variation on human polyadenylation using APARENT2" (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02799-4). Two versions of the model are available:</p> <p>(a) aparent_all_libs_resnet_no_clinvar_wt_ep_5.h5: The originally trained APARENT2 model.<br> (b) aparent_all_libs_resnet_no_clinvar_wt_ep_5_var_batch_size_inference_mode_no_drop.h5: Identical weights and predictions as model (a), but the normalization layers have been set to inference mode and the dropout layers have been removed (thus making it compatible with the scrambler pipeline).</p>
Deciphering the Impact of Genetic Variation on Human Polyadenylation using APARENT2
GEO Series GSE214825. Homo sapiens. 12 samples. Type: Other.
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