ArticleeLife2017
Systematic morphological profiling of human gene and allele function via Cell Painting.
Article in eLife, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
What it found
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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.
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Who cites it
101 citing papers in PubMed, 186 citations in OpenAlex.
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- Data modeling the interplay between single-cell shape, single-cell protein expression, and tissue state.Cell reports methods · 2026Article
- Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation.Molecular systems biology · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Retrieval-Based Evaluation of Cell Painting Feature Spaces Reveals Differences in the Preservation of Biologically Meaningful Phenotypic Similarity.International journal of molecular sciences · 2026Article
- A comprehensive pharmacological survey across heterogeneous patient-derived glioblastoma stem cell models.iScience · 2026Article
- Identifying and targeting abnormal mitochondrial localization associated with psychosis.bioRxiv : the preprint server for biology · 2026Article
- A scoping study of the whole-cell imaging literature as a foundation for the emerging field of cell anatomy.BMC biology · 2026Article
- A pooled Cell Painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning.Nature communications · 2025Article
- PhenoProfiler: advancing phenotypic learning for image-based drug discovery.Nature communications · 2025Article
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
- Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation.bioRxiv : the preprint server for biology · 2025Article
- Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer.Science advances · 2025Article
- Functional Neurogenomics to Dissect Disease Mechanisms Across Models.Annual review of genomics and human genetics · 2025Review
- Morphological map of under- and overexpression of genes in human cells.Nature methods · 2025Article
- MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery.bioRxiv : the preprint server for biology · 2025Article
- Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion.Nature communications · 2025Article
- Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.Cell systems · 2025Article
- Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles.Nature communications · 2025Article
- A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field.bioRxiv : the preprint server for biology · 2025Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation-based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/c-REL negative regulation of YAP1/WWTR1-responsive pathways. We confirmed this discovery of functional connectivity between the NF-κB pathway and Hippo pathway effectors at the transcriptional level, thereby expanding knowledge of these two signaling pathways that critically regulate tumor initiation and progression. We make the images and raw data publicly available, providing an initial morphological map of major biological pathways for future study.
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Registered trials
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.