ArticleProceedings of the National Academy of Sciences of the United States of America2012
Regulatory element copy number differences shape primate expression profiles.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- Article
- Segmental copy number amplifications are more stable than aneuploidies in the absence of selection.Molecular biology and evolution · 2026Article
- A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.bioRxiv : the preprint server for biology · 2025Article
- The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees.Genome biology · 2023Article
- Genomic structural variation: A complex but important driver of human evolution.American journal of biological anthropology · 2023Review
- Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics.PLoS biology · 2022Article
- Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats.Frontiers in genetics · 2021Article
- Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.Science (New York, N.Y.) · 2020Article
- Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.Genome research · 2020Article
- Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.Genes · 2020Article
- Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants.Nature communications · 2019Article
- Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.Genome biology and evolution · 2019Article
- Single-cell copy number variant detection reveals the dynamics and diversity of adaptation.PLoS biology · 2018Article
- Whole thorax irradiation of non-human primates induces persistent nuclear damage and gene expression changes in peripheral blood cells.PloS one · 2018Article
- The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence.BMC evolutionary biology · 2016Article
- Genomic medicine goes mainstream.NPJ genomic medicine · 2016Article
- Allele-specific copy-number discovery from whole-genome and whole-exome sequencing.Nucleic acids research · 2015Article
- Comparative studies of gene regulatory mechanisms.Current opinion in genetics & development · 2014Review
- Comparative analysis of pseudogenes across three phyla.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.Genome biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
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.