We are analyzing https://link.springer.com/article/10.1186/s13059-018-1414-4.

Title:
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data | Genome Biology
Description:
Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe ‘Quantification of APA’ (QAPA), a method that infers APA from conventional RNA-seq data. QAPA is faster and more sensitive than other methods. Application of QAPA reveals discrete, temporally coordinated APA programs during neurogenesis and that there is little overlap between genes regulated by alternative splicing and those by APA. Modeling of these data uncovers an APA sequence code. QAPA thus enables the discovery and characterization of programs of regulated APA using conventional RNA-seq.
Website Age:
28 years and 1 months (reg. 1997-05-29).

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Keywords {🔍}

polya, pubmed, apa, utr, site, genes, data, article, google, scholar, sites, rnaseq, qapa, expression, cas, ppau, alternative, gene, central, utrs, proximal, polyadenylation, features, methods, lengthening, analysis, isoforms, fig, usage, mrna, end, events, model, additional, isoform, distal, reads, sequencing, genome, method, set, shortening, samples, overlap, file, rna, human, differential, div, annotated,

Topics {✒️}

$$ {pau}_{ig}=\frac{e_{ig}}{\sum \limits_j{ enzyme-mgatp-rna ternary complex article download pdf steady-state mrna expression steady-state gene expression method-specific grid search achieve tissue-specific expression rna-binding protein motifs rna-seq read mappings simulating rna-seq datasets vast-tools diff module alternative pre-mrna splicing tissue-specific alternative polyadenylation synthetic rna-seq dataset conventional rna-seq data pre-mrna 3′-end processing skeletal rna-seq datasets longitudinal rna-seq data rna-seq data support fast gapped-read alignment rna-seq read coverage simulated rna-seq data high-throughput sequencing gene-set enrichment visualization substantial steady-state rna-seq samples divided produces position-specific probabilities steady-state expression /gu-rich region downstream employ high-throughput rapid reference-based approach potential cognate trans-factors extracting common keywords method-specific data preparation full size image additional post-transcriptional mechanisms rna-seq human brain sided kolmogorov–smirnov test pre-processed “final” datasets rna-seq reveal }_{jg}}\ast 100 $$ pre-processing steps required creative commons license privacy choices/manage cookies human tissue transcriptomes rna-seq-based methods machine learning algorithms sites involves interactions berg mg macdonald cc

Questions {❓}

AU-rich elements and associated factors: are there unifying principles?

Schema {🗺️}

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         headline:QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
         description:Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe ‘Quantification of APA’ (QAPA), a method that infers APA from conventional RNA-seq data. QAPA is faster and more sensitive than other methods. Application of QAPA reveals discrete, temporally coordinated APA programs during neurogenesis and that there is little overlap between genes regulated by alternative splicing and those by APA. Modeling of these data uncovers an APA sequence code. QAPA thus enables the discovery and characterization of programs of regulated APA using conventional RNA-seq.
         datePublished:2018-03-28T00:00:00Z
         dateModified:2018-03-28T00:00:00Z
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            High-throughput RNA sequencing
            Alternative polyadenylation
            Machine learning
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
      description:Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe ‘Quantification of APA’ (QAPA), a method that infers APA from conventional RNA-seq data. QAPA is faster and more sensitive than other methods. Application of QAPA reveals discrete, temporally coordinated APA programs during neurogenesis and that there is little overlap between genes regulated by alternative splicing and those by APA. Modeling of these data uncovers an APA sequence code. QAPA thus enables the discovery and characterization of programs of regulated APA using conventional RNA-seq.
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         High-throughput RNA sequencing
         Alternative polyadenylation
         Machine learning
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Department of Molecular Genetics, University of Toronto, Toronto, Canada
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