Evidence map›Paper›PMID 40580499›Full record

ArticleG3 (Bethesda, Md.)2025

PARPAL: PARalog Protein redistribution using Abundance and Localization in yeast database.

Brittany M Greco, Gerardo Zapata, Rohan Dandage, Mikhail Papkov, Vanessa Pereira, François Lefebvre, Guillaume Bourque, Leopold Parts, Elena Kuzmin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2025. 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. 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

9 authors.

Brittany M GrecoDepartment of Biology, Concordia University, 7141 Sherbrooke St W, Montreal, QC, Canada H4B 1R6.
Gerardo ZapataCanadian Centre for Computational Genomics (C3G), McGill University, 1010 Sherbrooke St W, Montreal, QC, Canada H3A 2R7.
Rohan DandageDepartment of Biology, Concordia University, 7141 Sherbrooke St W, Montreal, QC, Canada H4B 1R6.
Mikhail PapkovInstitute of Computer Science, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia.
Vanessa PereiraDepartment of Biology, Concordia University, 7141 Sherbrooke St W, Montreal, QC, Canada H4B 1R6.
François LefebvreCanadian Centre for Computational Genomics (C3G), McGill University, 1010 Sherbrooke St W, Montreal, QC, Canada H3A 2R7.
Guillaume BourqueCanadian Centre for Computational Genomics (C3G), McGill University, 1010 Sherbrooke St W, Montreal, QC, Canada H3A 2R7.ORCID 0000-0002-3933-9656
Leopold PartsInstitute of Computer Science, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia.
Elena KuzminDepartment of Biology, Concordia University, 7141 Sherbrooke St W, Montreal, QC, Canada H4B 1R6.ORCID 0000-0002-7479-9308

Funding

Canada Foundation for Innovation CFI 41563Canada Research Chair program CRC2021-00031Computing resources and data storage servicesDigital Research Alliance of CanadaHigh-Performance Computing CenterNatural Sciences and Engineering Research Council RGPIN-2022-04674Revvity Inc. VLTAT19682University of TartuWellcome TrustWellcome Trust 220540/Z/20/A
6 · The paper itself

Abstract

Whole-genome duplication (WGD) events are common across various organisms; however, the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WGD paralog provides insight into sources of gene retention. Here, we describe PARPAL (PARalog Protein Redistribution using Abundance and Localization in Yeast), a web database that houses results of high-content screening and deep learning neural network analysis of the redistribution of 164 proteins reflecting how their subcellular localization and protein abundance change in response to their paralog deletion in the budding yeast, Saccharomyces cerevisiae. We interrogated a total of 82 paralog pairs in 2 genetic backgrounds for a total of ∼3,500 micrographs of ∼460,000 cells. For example, Skn7-Hms2 exhibited dependent redistribution, and Cue1-Cue4 showed compensatory redistribution response. PARPAL also links to other studies on trigenic interactions, protein-protein interactions and protein abundance. PARPAL is available at https://parpal.c3g-app.sd4h.ca and is a valuable resource for the yeast community interested in understanding the retention and evolution of paralogs and can help researchers to investigate protein dynamics of paralogs in other organisms.

Indexed as

Saccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsProtein TransportSaccharomyces cerevisiae Proteinsbudding yeastdeep neural networkduplicated geneshigh-content screeningparalogsphenomicsprotein abundanceprotein subcellular localizationSaccharomyces cerevisiae

Identifiers

PMID40580499
PMCPMC12405880

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.