ArticlePLoS genetics2012
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
136 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- The superpowers of imprinting control regions.Genome research · 2026Review
- Long-read sequencing disentangles isoform complexity at allele-specific loci.Scientific reports · 2025Article
- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
- Article
- Imprinted Genes: Genomic Conservation, Transcriptomic Dynamics and Phenomic Significance in Health and Diseases.International journal of biological sciences · 2023Review
- Systematic investigation of imprinted gene expression and enrichment in the mouse brain explored at single-cell resolution.BMC genomics · 2022Article
- The Defects of Epigenetic Reprogramming in Dox-Dependent Porcine-iPSCs.International journal of molecular sciences · 2022Article
- DNA Methylation Analysis of Imprinted Genes in the Cortex and Hippocampus of Cross-Fostered Mice Selectively Bred for Increased Voluntary Wheel-Running.Behavior genetics · 2022Article
- BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes.Communications biology · 2022Article
- Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.G3 (Bethesda, Md.) · 2021Article
- Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs.Scientific reports · 2021Article
- Conservation of Imprinting and Methylation ofAnimals : an open access journal from MDPI · 2021Article
- Features and mechanisms of canonical and noncanonical genomic imprinting.Genes & development · 2021Review
- Feasibility of predicting allele specific expression from DNA sequencing using machine learning.Scientific reports · 2021Article
- Understanding experiments and research practices for reproducibility: an exploratory study.PeerJ · 2021Article
- Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart.Frontiers in cell and developmental biology · 2021Article
- Article
- Review
76 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA-Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin-dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates.
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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.