ArticleBiomedicines2020
Meta-Analysis of Hypoxic Transcriptomes from Public Databases.
Article in Biomedicines, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 3 of them syntheses that pooled it.
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.
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
29 citing papers in PubMed, 3 syntheses or guidelines pooled it, 62 citations in OpenAlex.
- Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer.BMC medical genomics · 2023Pooled it
- Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples.International journal of molecular sciences · 2023Pooled it
- Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set.Life science alliance · 2023Pooled it
- Engineered atopic dermatitis models for recreating hypoxic conditions in atopic dermatitis microenvironments.Bioactive materials · 2026Article
- Differential roles of the type I and II secretion systems for the intracellular ABC141 Acinetobacter baumannii infection, which elicits an atypical hypoxia response in endothelial cells.PLoS pathogens · 2026Article
- Physiological Differences Underlying Divergent Hypoxia Responses and Altitude Adaptations in Humans, Rats and Mice.Comprehensive Physiology · 2025Review
- Multiomics Analysis Reveals Role of ncRNA in Hypoxia of Mouse Brain Microvascular Endothelial Cells.International journal of molecular sciences · 2025Article
- Distinct methylomic signatures of high-altitude acclimatization and adaptation in the Tibetan Plateau.Cell discovery · 2025Article
- Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing.International journal of molecular sciences · 2025Review
- Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth.Genome research · 2025Article
- Hypoxia-inducible factor 2 regulates alveolar regeneration after repetitive injury in three-dimensional cellular and in vivo models.Science translational medicine · 2025Article
- Stc2a inhibits IGF-stimulated somatic growth in favor of organismal survival under hypoxic stress.Frontiers in endocrinology · 2025Article
- Molecular characterization and function of hif1a and fih1 in response to acute thermal stress in American shad (Alosa sapidissima).Fish physiology and biochemistry · 2024Article
- Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data.Animals : an open access journal from MDPI · 2024Article
- Sleep Disorder Kleine-Levin Syndrome (KLS) Joins the List of Polygenic Brain Disorders Associated with Obstetric Complications.Cellular and molecular neurobiology · 2023Review
- Local YB-1, Epo, and EpoR concentrations in fractured bones: results from a porcine model of multiple trauma.European journal of medical research · 2023Article
- Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.iScience · 2022Article
- Formal Meta-Analysis of Hypoxic Gene Expression Profiles Reveals a Universal Gene Signature.Biomedicines · 2022Article
- Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia.Life (Basel, Switzerland) · 2022Article
- N-VEGF, the Autoregulatory Arm of VEGF-A.Cells · 2022Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted a meta-analysis of the RNA-seq data from the hypoxic transcriptomes archived in public databases. In view of methodological variability of archived data in the databases, we first manually curated RNA-seq data from appropriate pairs of transcriptomes before and after hypoxic stress. These included 128 human and 52 murine transcriptome pairs. We classified the results of experiments for each gene into three categories: upregulated, downregulated, and unchanged. Hypoxic transcriptomes were then compared between humans and mice to identify common hypoxia-responsive genes. In addition, meta-analyzed hypoxic transcriptome data were integrated with public ChIP-seq data on the known human HIFs, HIF-1 and HIF-2, to provide insights into hypoxia-responsive pathways involving direct transcription factor binding. This study provides a useful resource for hypoxia research. It also demonstrates the potential of a meta-analysis approach to public gene expression databases for selecting candidate genes from gene expression profiles generated under various experimental conditions.
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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.