Evidence map›Paper›PMID 40775081›Full record

ArticleNature methods2025

Morphological map of under- and overexpression of genes in human cells.

Srinivas Niranj Chandrasekaran, Eric Alix, John Arevalo, Adriana Borowa, Patrick J Byrne, William G Charles, Zitong S Chen, Beth A Cimini, Boxiong Deng, John G Doench and 46 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. A Framework for Autonomous AI-Driven Drug Discovery.bioRxiv : the preprint server for biology · 2026
    Article
  6. Insulin Resistance and Inflammation.International journal of molecular sciences · 2026
    Review
  7. Article
  8. Article
  9. 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

56 authors.

Srinivas Niranj ChandrasekaranBroad Institute, Cambridge, MA, USA.
Eric AlixRevvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.
John ArevaloBroad Institute, Cambridge, MA, USA.
Adriana BorowaArdigen S.A, Kraków, Poland.
Patrick J ByrneBroad Institute, Cambridge, MA, USA.
William G CharlesEvotec SE, Hamburg, Germany.ORCID http://orcid.org/0000-0001-7948-253X
Zitong S ChenBroad Institute, Cambridge, MA, USA.
Beth A CiminiBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9640-9318
Boxiong DengStanford University, Stanford, CA, USA.
John G DoenchBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-3707-9889
Jessica D EwaldBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7555-736X
Briana FritchmanBroad Institute, Cambridge, MA, USA.
Colin J FullerSpring Science, San Carlos, CA, USA.ORCID http://orcid.org/0009-0007-9490-6020
Jedidiah GaetzPlex Research Inc., Cambridge, MA, USA.
Amy GoodaleBroad Institute, Cambridge, MA, USA.
Marzieh HaghighiBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0867-8364
Yu HanBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-5507-9228
Zahra HanifehlouKsilink, Strasbourg, France.
Holger HennigEvotec SE, Hamburg, Germany.
Desiree HernandezBroad Institute, Cambridge, MA, USA.
Christina B JacobKsilink, Strasbourg, France.
Tim JamesEvotec SE, Hamburg, Germany.
Tomasz JetkaArdigen S.A, Kraków, Poland.
Alexandr A KalininBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-4563-3226
Ben KomaloSpring Science, San Carlos, CA, USA.
Maria Kost-AlimovaBroad Institute, Cambridge, MA, USA.
Tomasz KrawiecArdigen S.A, Kraków, Poland.
Brittany A MarionBroad Institute, Cambridge, MA, USA.
Glynn MartinRevvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.
Nicola Jane McCarthyRevvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.ORCID http://orcid.org/0000-0001-6990-3943
Lisa MillerBroad Institute, Cambridge, MA, USA.
Arne MonseesEvotec SE, Hamburg, Germany.
Nikita MoshkovBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-5823-4884
Alán F MuñozBroad Institute, Cambridge, MA, USA.
Arnaud OgierKsilink, Strasbourg, France.
Magdalena OtrockaArdigen S.A, Kraków, Poland.
Krzysztof RatajArdigen S.A, Kraków, Poland.
David E RootBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-5122-861X
Francesco RubboSpring Science, San Carlos, CA, USA.ORCID http://orcid.org/0000-0001-5170-3652
Simon ScraceRevvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.
Douglas W SelingerPlex Research Inc., Cambridge, MA, USA.ORCID http://orcid.org/0009-0005-3031-0856
Rebecca A SenftBroad Institute, Cambridge, MA, USA.
Peter SommerKsilink, Strasbourg, France.ORCID http://orcid.org/0000-0001-9241-5710
Amandine ThibaudeauKsilink, Strasbourg, France.
Sarah TrisorusSpring Science, San Carlos, CA, USA.
Rahul Valiya VeettilEvotec SE, Hamburg, Germany.ORCID http://orcid.org/0000-0003-2426-5989
William J Van TrumpSpring Science, San Carlos, CA, USA.
Sui WangStanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1563-9117
Michał WarchołArdigen S.A, Kraków, Poland.
Erin WeisbartBroad Institute, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6437-2458
Amélie WeissKsilink, Strasbourg, France.
Michael WiestSpring Science, San Carlos, CA, USA.
Agata ZarembaArdigen S.A, Kraków, Poland.
Andrei ZinovyevEvotec SE, Hamburg, Germany.ORCID http://orcid.org/0000-0002-9517-7284
Shantanu SinghBroad Institute, Cambridge, MA, USA. shantanu@broadinstitute.org.ORCID http://orcid.org/0000-0003-3150-3025
Anne E CarpenterBroad Institute, Cambridge, MA, USA. anne@broadinstitute.org.ORCID http://orcid.org/0000-0003-1555-8261

Funding

Extracting rich information from biological imagesR35GM122547 · NIGMS · BROAD INSTITUTE, INC. · PI Anne E. Carpenter · 2017 to 2026
$6.2M
Opera Phenix high-throughput microplate confocal imager for high-content screeningS10OD026839 · OD · BROAD INSTITUTE, INC. · PI WAGNER, BRIDGET K · 2019 to 2019
$1.0M
NIGMS NIH HHS R35 GM122547NIH HHS S10 OD026839U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health) MIRA R35 GM122547
6 · The paper itself

Abstract

Cell Painting images offer valuable insights into a cell's state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames) and knocking out 7,975 genes (using CRISPR-Cas9). Here we mitigated technical artifacts by rigorously evaluating data processing options and validated the dataset's robustness and biological relevance. Analysis of phenotypic profiles revealed previously undiscovered gene clusters and functional relationships, including those associated with mitochondrial function, cancer and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering previously unknown functions.

Indexed as

Single-Cell AnalysisCell Line, TumorCRISPR-Cas SystemsHumans

Identifiers

PMID40775081
PMCPMC12439680

What OpenQuestion holds

Textmetadata
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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.