Evidence map›Paper›PMID 38132320›Full record

ArticleBiology2023

Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue.

Anna Kozlova, Elizaveta Sarygina, Kseniia Deinichenko, Sergey Radko, Konstantin Ptitsyn, Svetlana Khmeleva, Leonid Kurbatov, Pavel Spirin, Vladimir Prassolov, Ekaterina Ilgisonis and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biology, 2023. 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
0.3field-weighted citation impact, top 35% 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.

  1. Article
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

12 authors at 2 institutions in 1 country.

Anna KozlovaInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.ORCID 0000-0002-2147-6679
Elizaveta SaryginaInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Kseniia DeinichenkoInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Sergey RadkoInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Konstantin PtitsynInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Svetlana KhmelevaInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Leonid KurbatovInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Pavel SpirinDepartment of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia.ORCID 0000-0002-0610-5079
Vladimir PrassolovDepartment of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia.ORCID 0000-0002-2429-6649
Ekaterina IlgisonisInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Andrey LisitsaInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Elena PonomarenkoInstitute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia.
Institute of Biomedical Chemistry · RUEngelhardt Institute of Molecular Biology · RU

Funding

The Ministry of Education and Science of the Russian Federation 075-15-2021-933
6 · The paper itself

Abstract

The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS-the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.

Indexed as

alternative splicingbiological pathwaysdegree of alternative splicingHepG2 and Huh7 cellshuman liver tissuelong-read sequencingsplice variants abundancetissue specificity indextranscriptome

Identifiers

PMID38132320
PMCPMC10740679
OpenAlexW4389398524

What Socratic 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 Socratic graph.