SynthesisNucleic acids research2017
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker.
Synthesis in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 2 of them syntheses that pooled it.
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
21 citing papers in PubMed, 2 syntheses or guidelines pooled it, 35 citations in OpenAlex.
- Comparative meta-analysis of transcriptomic studies in spinal muscular atrophy: comparison between tissues and mouse models.BMC medical genomics · 2024Pooled it
- Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses.Journal of biological rhythms · 2023Pooled it
- Molecular correlates of sleep deprivation in the mouse brain identified by meta-analysis of microarray data.Neurobiology of sleep and circadian rhythms · 2026Article
- Co-expression network analysis reveals repression ofbioRxiv : the preprint server for biology · 2026Article
- Toward dissection of diverse neural components in the suprachiasmatic nucleus (SCN) pacemaker network.Neurobiology of sleep and circadian rhythms · 2026Article
- Monoallelic gene expression in developing cells increases genetic noise and Shannon entropy.Communications biology · 2025Article
- Dnajc5b contributes to male fertility by maintaining the mitochondrial functions and autophagic homeostasis during spermiogenesis.Cellular and molecular life sciences : CMLS · 2025Article
- Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock.Genome research · 2023Article
- Timed exercise stabilizes behavioral rhythms but not molecular programs in the brain's suprachiasmatic clock.iScience · 2023Article
- Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease during disease progression in Trypanosoma. b. brucei infected CD1 mouse brains.PLoS neglected tropical diseases · 2021Article
- Single-cell transcriptomics of suprachiasmatic nuclei reveal a Prokineticin-driven circadian network.The EMBO journal · 2021Article
- Targeted Disruption of theInternational journal of molecular sciences · 2021Article
- ON-bipolar cell gene expression during retinal degeneration: Implications for optogenetic visual restoration.Experimental eye research · 2021Article
- Genesis of the Master Circadian Pacemaker in Mice.Frontiers in neuroscience · 2021Review
- Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration.Frontiers in cell and developmental biology · 2020Article
- Circuit development in the master clock network of mammals.The European journal of neuroscience · 2020Review
- Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia.PLoS genetics · 2019Article
- Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.Journal of proteome research · 2019Article
- Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms.Nature communications · 2019Article
- Generation of circadian rhythms in the suprachiasmatic nucleus.Nature reviews. Neuroscience · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. A total of 79 microarrays were used (24 SCN and 55 WB samples, 4 different microarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB). 31 684 MGI gene symbols had data for at least one platform. Meta-analysis using a random effects model for weighting individual effect sizes (derived from differential expression between relevant SCN and WB samples) reliably detected known SCN markers. SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers.
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.