ArticleMatrix biology plus2021
Extracellular matrix gene expression signatures as cell type and cell state identifiers.
Article in Matrix biology plus, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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
14 citing papers in PubMed, 24 citations in OpenAlex.
- Dynamic profiling of BMSC-dECM reveals accumulation of core matrisome proteins suppresses osteogenic differentiation and bone regeneration.Journal of advanced research · 2026Article
- Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis.Nature communications · 2025Article
- Single-Nucleus RNA Sequencing Reveals the Transcriptome Profiling of Ovarian Cells in AdolescentAnimals : an open access journal from MDPI · 2024Article
- FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics.Nature methods · 2024Article
- Analysis of cancer cell line and tissue RNA sequencing data reveals an essential and dark matrisome.Matrix biology plus · 2024Article
- Extracellular matrix protein composition dynamically changes during murine forelimb development.iScience · 2024Article
- Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.Nature communications · 2024Article
- Article
- Extracellular Matrix Dynamics as an Emerging yet Understudied Hallmark of Aging and Longevity.Aging and disease · 2023Review
- ClonoCluster: A method for using clonal origin to inform transcriptome clustering.Cell genomics · 2023Article
- Review
- Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma.Genome medicine · 2022Article
- Cell types as species: Exploring a metaphor.Frontiers in plant science · 2022Review
- Longevity-Promoting Pathways and Transcription Factors Respond to and Control Extracellular Matrix Dynamics During Aging and Disease.Frontiers in aging · 2022Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development,
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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.