ArticleGenome biology2012
The GENCODE pseudogene resource.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers, 1 of them a synthesis that pooled it.
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Who cites it
203 citing papers in PubMed, 1 synthesis or guideline pooled it, 347 citations in OpenAlex.
- Competing endogenous RNA (ceRNA) networks in Parkinson's disease: A systematic review.Frontiers in cellular neuroscience · 2023Pooled it
- Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.Human molecular genetics · 2015Trial
- Functional roles and clinical implications of pseudogenes signatures as emerging biomarkers in cancer.Discover oncology · 2026Review
- Application of Proteogenomic Approaches for Refinement of the Entamoeba histolytica Reference Genome Using High Resolution Mass-Spectrometry Data.Acta parasitologica · 2026Article
- A new mechanism underlying mitochondrial dysfunction in schizophrenia - attenuated mRNA transport of the complex I subunit NDUFV2 by its pseudogene NDUFV2P1.Schizophrenia (Heidelberg, Germany) · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Comparative chloroplast genomes of Hamamelidaceae: genome evolution and phylogenomic implications.BMC plant biology · 2026Article
- Epigenetic characterization of pseudogenes across human tissues.Genome research · 2026Article
- ComprehensiveNon-coding RNA · 2026Article
- Defective biological networks associated with pseudogene-derived lncRNAs in cancer drug resistance: Promising prospects for their clinical targets in cancer therapy.Genes & diseases · 2026Review
- PETScan: score-based genome-wide association analysis of RNA-Seq and ATAC-Seq data.Bioinformatics (Oxford, England) · 2026Article
- Integrating Long-Read Nanopore Sequencing for Precision Resolution of Genomic Variants in Dystonia.Movement disorders : official journal of the Movement Disorder Society · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- The Fine Structure of Genome Statistics-The Frequency and Size.Life (Basel, Switzerland) · 2025Article
- Global genomic and antimicrobial resistance profiling of Neisseria gonorrhoeae: Insights from whole genome sequencing and minimum inhibitory concentration analysis.PLoS neglected tropical diseases · 2025Article
- Distinctive chromosomal, mutational and transcriptional profiling in colon versus rectal cancers.Journal of translational medicine · 2025Article
- The role of long non-coding RNAs in lung cancer metastasis: Molecular mechanisms, pathogenesis and clinical implications.Clinical and translational medicine · 2025Review
- Tick genomics through a Nanopore: a low-cost approach for tick genomics.BMC genomics · 2025Article
- Deciphering Cancer Complexity: Integrative Proteogenomics and Proteomics Approaches for Biomarker Discovery.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Competing endogenous RNAs network dysregulation in oral cancer: a multifaceted perspective on crosstalk and competition.Cancer cell international · 2024Review
143 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 6 institutions in 4 countries.
Funding
Abstract
backgroundPseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data.
resultsAs part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection.
conclusionsAt one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.
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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.