Evidence map›Paper›PMID 39242990›Full record

ArticleBMC bioinformatics2024

Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.

Sarah E Fumagalli, Sean Smith, Tigran Ghazanchyan, Douglas Meyer, Rahul Paul, Collin Campbell, Luis Santana-Quintero, Anton Golikov, Juan Ibla, Haim Bar and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 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
–field-weighted citation impact
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.

  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

15 authors.

Sarah E Fumagalli *Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Sean Smith *High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Tigran Ghazanchyan *High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Douglas MeyerHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Rahul PaulHigh-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Collin CampbellHigh-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Luis Santana-QuinteroHigh-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Anton GolikovHigh-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Juan IblaDepartment of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
Haim BarDepartment of Statistics, University of Connecticut, Storrs, CT, USA.
Anton A KomarDepartment of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA.
Ryan C HuntHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Brian LinHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
Michael DiCuccio, Rockville, USA.
Chava Kimchi-SarfatyHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA. chava.kimchi-sarfaty@fda.hhs.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Mouse (Mus musculus) models have been heavily utilized in developmental biology research to understand mammalian embryonic development, as mice share many genetic, physiological, and developmental characteristics with humans. New explorations into the integration of temporal (stage-specific) and transcriptional (tissue-specific) data have expanded our knowledge of mouse embryo tissue-specific gene functions. To better understand the substantial impact of synonymous mutational variations in the cell-state-specific transcriptome on a tissue's codon and codon pair usage landscape, we have established a novel resource-Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs). This webpage not only offers codon and codon pair usage, but also GC, dinucleotide, and junction dinucleotide usage, encompassing four strains, 15 murine embryonic tissue groups, 18 Theiler stages, and 26 embryonic days. Here, we leverage Mouse Embryo CoCoPUTs and employ the use of heatmaps to depict usage changes over time and a comparison to human usage for each strain and embryonic time point, highlighting unique differences and similarities. The usage similarities found between mouse and human central nervous system data highlight the translation for projects leveraging mouse models. Data for this analysis can be directly retrieved from Mouse Embryo CoCoPUTs. This cutting-edge resource plays a crucial role in deciphering the complex interplay between usage patterns and embryonic development, offering valuable insights into variation across diverse tissues, strains, and stages. Its applications extend across multiple domains, with notable advantages for biotherapeutic development, where optimizing codon usage can enhance protein expression; one can compare strains, tissues, and mouse embryonic stages in one query. Additionally, Mouse Embryo CoCoPUTs holds great potential in the field of tissue-specific genetic engineering, providing insights for tailoring gene expression to specific tissues for targeted interventions. Furthermore, this resource may enhance our understanding of the nuanced connections between usage biases and tissue-specific gene function, contributing to the development of more accurate predictive models for genetic disorders.

Indexed as

TranscriptomeAnimalsCodon UsageEmbryo, MammalianEmbryonic DevelopmentHumansMiceCodon pair usageCodon usageDinucleotide usageEmbryonic dayGC contentJunction dinucleotide usageMouse embryo CoCoPUTsTheiler stageTissue-specificTranscriptomic-weighted embryo data

Identifiers

PMID39242990
PMCPMC11380194

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.