Evidence map›Paper›PMID 36865326›Full record

ArticlebioRxiv : the preprint server for biology2023

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.

Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 2 countries.

Arjun PatelDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Dominic McGrossoDepartment of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
Ying HefnerDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Anaamika CampeauDepartment of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
Anand V SastryDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Svetlana MauryaDepartment of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
Kevin RychelDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
David J GonzalezSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Bernhard O PalssonDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
University of California San Diego · USNovo Nordisk Foundation · DK

Funding

GENOMICALLY BASED MODELS FOR ANTIBIOTIC DEVELOPMENTR01GM057089 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PALSSON, BERNHARD O · 1998 to 2021
$6.9M
NIGMS NIH HHS R01 GM057089
6 · The paper itself

Abstract

It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigated whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions could be modularized in the same way to reveal novel relationships between their compositions. We found that; 1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, 2) the modules in the proteome often represent combinations of modules from the transcriptome, 3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and 4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.

Identifiers

PMID36865326
PMCPMC9980150
OpenAlexW4321437894

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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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.