ArticleCell research2016
A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer.
Article in Cell research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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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.
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.
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Who cites it
61 citing papers in PubMed, 1 synthesis or guideline pooled it, 119 citations in OpenAlex.
- Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer.Genome medicine · 2023Pooled it
- Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Lack of evidence for transcription-to-RNA maturation lags across G1-to-G2-phase boundary in fibroblasts.Life science alliance · 2026Article
- Charting the multilevel molecular response to palbociclib in ER-positive breast cancer.NAR cancer · 2026Article
- Splicing as an integrative layer linking cell cycle regulation, epigenetic dynamics, and environmental responses in plants.Frontiers in plant science · 2026Review
- Dynamics and variegation in the Treg response to Interleukin-2.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Unsupervised Machine Learning Reveals Temporal Components of Gene Expression in HeLa Cells Following Release from Cell Cycle Arrest.International journal of molecular sciences · 2025Article
- E2F1 induces a G0-G1 reentry transcriptional program without changing chromatin accessibility.bioRxiv : the preprint server for biology · 2025Article
- Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts.bioRxiv : the preprint server for biology · 2025Article
- The chronODE framework for modelling multi-omic time series with ordinary differential equations and machine learning.Nature communications · 2025Article
- Plasmodium falciparum infection induces T cell tolerance that is associated with decreased disease severity upon re-infection.The Journal of experimental medicine · 2025Article
- Early transcriptional effects of inflammatory cytokines reveal highly redundant cytokine networks.The Journal of experimental medicine · 2025Article
- TAAR9 knockout increases hippocampal serotonin and alters grooming behavior in rats.Frontiers in pharmacology · 2025Article
- CDK4 as a Prognostic Marker of Hepatocellular Carcinoma and CDK4 Inhibitors as Potential Therapeutics.Current medicinal chemistry · 2025Article
- Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach.Molecular systems biology · 2024Article
- GRHL2 regulates keratinocyte EMT-MET dynamics and scar formation during cutaneous wound healing.Cell death & disease · 2024Article
- CD99 contributes to the EWS::FLI1 transcriptome by specifically affecting FOXM1-targets involved in the G2/M cell cycle phase, thus influencing the Ewing sarcoma genetic landscape.Journal of cell communication and signaling · 2024Article
- MCM8 interacts with DDX5 to promote R-loop resolution.The EMBO journal · 2024Article
- Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.Nature communications · 2024Article
- Adult Human, but Not Rodent, Spermatogonial Stem Cells Retain States with a Foetal-like Signature.Cells · 2024Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
Abstract
Progression through the cell cycle is largely dependent on waves of periodic gene expression, and the regulatory networks for these transcriptome dynamics have emerged as critical points of vulnerability in various aspects of tumor biology. Through RNA-sequencing of human cells during two continuous cell cycles (>2.3 billion paired reads), we identified over 1 000 mRNAs, non-coding RNAs and pseudogenes with periodic expression. Periodic transcripts are enriched in functions related to DNA metabolism, mitosis, and DNA damage response, indicating these genes likely represent putative cell cycle regulators. Using our set of periodic genes, we developed a new approach termed "mitotic trait" that can classify primary tumors and normal tissues by their transcriptome similarity to different cell cycle stages. By analyzing >4 000 tumor samples in The Cancer Genome Atlas (TCGA) and other expression data sets, we found that mitotic trait significantly correlates with genetic alterations, tumor subtype and, notably, patient survival. We further defined a core set of 67 genes with robust periodic expression in multiple cell types. Proteins encoded by these genes function as major hubs of protein-protein interaction and are mostly required for cell cycle progression. The core genes also have unique chromatin features including increased levels of CTCF/RAD21 binding and H3K36me3. Loss of these features in uterine and kidney cancers is associated with altered expression of the core 67 genes. Our study suggests new chromatin-associated mechanisms for periodic gene regulation and offers a predictor of cancer patient outcomes.
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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.