ArticlePLoS computational biology2010
Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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.
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.
Who cites it
54 citing papers in PubMed, 3 citations in OpenAlex.
- Review
- Lipocalin-2 in Triple-Negative Breast Cancer: A Review of Its Pathophysiological Role in the Metastatic Cascade.International journal of molecular sciences · 2025Review
- Application of Machine Learning in Predicting Osteogenic Differentiation of Mesenchymal Stem Cells.Bioengineering (Basel, Switzerland) · 2025Review
- Review
- 3D-Organoid-SwinNet: High-Content Profiling of 3D Organoids.IEEE journal of biomedical and health informatics · 2025Article
- Artificial intelligence-based analysis of time-lapse images of sphere formation and process of plate adhesion and spread of pancreatic cancer cells.Frontiers in cell and developmental biology · 2023Article
- CD36International journal of molecular sciences · 2022Article
- Article
- Detecting prognostic biomarkers of breast cancer by regularized Cox proportional hazards models.Journal of translational medicine · 2021Article
- Protein Ligands in the Secretome of CD36Cancers · 2021Article
- The not-so-sweet side of sugar: Influence of the microenvironment on the processes that unleash cancer.Biochimica et biophysica acta. Molecular basis of disease · 2020Review
- Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer.APL bioengineering · 2020Article
- Breast cancer models: Engineering the tumor microenvironment.Acta biomaterialia · 2020Review
- Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure.Bioinformatics (Oxford, England) · 2020Article
- YY1 is a cis-regulator in the organoid models of high mammographic density.Bioinformatics (Oxford, England) · 2020Article
- YKL-40/CHI3L1 facilitates migration and invasion in HER2 overexpressing breast epithelial progenitor cells and generates a niche for capillary-like network formation.In vitro cellular & developmental biology. Animal · 2019Article
- Agent-based model of multicellular tumor spheroid evolution including cell metabolism.The European physical journal. E, Soft matter · 2019Article
- Article
- The adaptor SASH1 acts through NOTCH1 and its inhibitor DLK1 in a 3D model of lumenogenesis involving CEACAM1.Experimental cell research · 2017Article
- The scaffold protein p140Cap limits ERBB2-mediated breast cancer progression interfering with Rac GTPase-controlled circuitries.Nature communications · 2017Article
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 3 institutions in 1 country.
Funding
Abstract
Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARgamma has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARgamma has been validated through two supporting biological assays.
Indexed as
Identifiers
What OpenQuestion holds
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.