vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.

Xingyu Bi, Wenbin Ye, Xin Cheng, Ning Yang, Xiaohui Wu

Open access · goldAbstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.5field-weighted citation impact, top 38% of its field

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 2 citations in OpenAlex.

Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025
Review

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 3 institutions in 3 countries.

Xingyu BiPasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China.

Wenbin YeDivision of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, United States.ORCID 0000-0002-7811-2710

Xin ChengPasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China.

Ning YangCollege of Industrial Design, Pukyong National University, Busan 48513, Korea.

Xiaohui WuPasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China.ORCID 0000-0003-0356-7785

Soochow University · CNPukyong National University · KRUniversity of California, Irvine · US

Funding

National Natural Science Foundation of China T2222007

6 · The paper itself

Abstract

motivationAlternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis.

resultsWe developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations. vizAPA also enables identification of genes with differential APA usage across biological samples and/or cell types. vizAPA provides four unique modules for extensively visualizing APA dynamics across biological samples and at the single-cell level. vizAPA could serve as a plugin in many routine APA analysis pipelines to augment studies for APA dynamics. AVAILABILITY AND IMPLEMENTATION: https://github.com/BMILAB/vizAPA.

Indexed as

Gene Expression RegulationPolyadenylation3' Untranslated RegionsEukaryota3' Untranslated Regions

Identifiers

PMID38485700

DOI10.1093/bioinformatics/btae099

PMCPMC10950478

OpenAlexW4392861050

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.