ArticleGenome research2012
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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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.
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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
35 citing papers in PubMed.
- Personalized single-cell transcriptomics reveals molecular diversity in Alzheimer's disease.Nature communications · 2026Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples.NAR genomics and bioinformatics · 2023Article
- LncDC: a machine learning-based tool for long non-coding RNA detection from RNA-Seq data.Scientific reports · 2022Article
- Non-coding antisense transcripts: fine regulation of gene expression in cancer.Computational and structural biotechnology journal · 2022Review
- HER2-PI9 and HER2-I12: two novel and functionally active splice variants of the oncogene HER2 in breast cancer.Journal of cancer research and clinical oncology · 2021Article
- GENCODE 2021.Nucleic acids research · 2021Article
- GENCODE reference annotation for the human and mouse genomes.Nucleic acids research · 2019Article
- Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3'-RACE and High-Throughput Sequencing.Molecules (Basel, Switzerland) · 2018Article
- HAfTs are novel lncRNA transcripts from aflatoxin exposure.PloS one · 2018Article
- TACO produces robust multisample transcriptome assemblies from RNA-seq.Nature methods · 2017Article
- Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency.BMC genomics · 2016Article
- lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts.Scientific reports · 2016Article
- Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).Nature communications · 2016Article
- Functional genomics of human brain development and implications for autism spectrum disorders.Translational psychiatry · 2015Review
- Creating reference gene annotation for the mouse C57BL6/J genome assembly.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.BMC genomics · 2015Article
- Discovery of a novel small secreted protein family with conserved N-terminal IGY motif in Dikarya fungi.BMC genomics · 2014Article
- Complex interactions of transcription factors in mediating cytokine biology in T cells.Immunological reviews · 2014Review
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.
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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.