Evidence map›Paper›PMID 39395408›Full record

ArticleCell genomics2024

Gene regulatory network inference from CRISPR perturbations in primary CD4

Joshua S Weinstock, Maya M Arce, Jacob W Freimer, Mineto Ota, Alexander Marson, Alexis Battle, Jonathan K Pritchard

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed, 1 pooled it
–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

14 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  5. Transcription-based comparison ofMicrobiology spectrum · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Joshua S WeinstockDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Maya M ArceGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Jacob W FreimerDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
Mineto OtaDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
Alexander MarsonGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: alex.marson@gladstone.ucsf.edu.
Alexis BattleDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA. Electronic address: ajbattle@jhu.edu.
Jonathan K PritchardDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA. Electronic address: pritch@stanford.edu.

Funding

Integration of genetic association mapping and functional data to elucidate genetic mechanisms of diseaseR01HG008140 · NHGRI · STANFORD UNIVERSITY · PI JONATHAN K PRITCHARD · 2016 to 2026
$7.3M
Restorative practice in repairing harm and promoting safe and inclusive practices in the laboratory.T32GM136547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Adrian Erlebacher, Anita Sil · 2020 to 2026
$4.5M
Modeling the dynamicimpact of rare and common genetic variation on gene expression anddiseaseR35GM139580 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BATTLE, ALEXIS · 2021 to 2025
$3.1M
NHGRI NIH HHS R01 HG008140NIGMS NIH HHS R35 GM139580NIGMS NIH HHS T32 GM136547
6 · The paper itself

Abstract

The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation has been challenging due to small effects, but experimental perturbations offer a complementary approach. Using CRISPR, we knocked out 84 genes in primary CD4

Indexed as

CD4-Positive T-LymphocytesGene Regulatory NetworksGenome-Wide Association StudyBayes TheoremClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsHistone-Lysine N-MethyltransferaseHumansImmune System DiseasesTranscription FactorsHistone-Lysine N-MethyltransferaseTranscription FactorsCRISPRgene regulatory networksGWASimmunologyinbornb errors of immunitynetwork inferenceRNA-seqT cells

Identifiers

PMID39395408
PMCPMC11605694

What OpenQuestion holds

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LicenceCC BY-NC
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.