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Critical evaluation of the FANTOM3 non-coding RNA transcripts
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
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2009 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 94, no 3, 169-176 p.Article in journal (Refereed) Published
Abstract [en]

We studied the genomic positions of 38,129 putative ncRNAs from the RIKEN dataset in relation to protein-coding genes. We found that the dataset has 41% sense, 6% antisense, 24% intronic and 29% intergenic transcripts. Interestingly, 17,678 (47%) of the FANTOM3 transcripts were found to potentially be internally primed from longer transcripts. The highest fraction of these transcripts was found among the intronic transcripts and as many as 77% or 6929 intronic transcripts were both internally primed and unspliced. We defined a filtered subset of 8535 transcripts that did not overlap with protein-coding genes, did not contain ORFs longer than 100 residues and were not internally primed. This dataset contains 53% of the FANTOM3 transcripts associated to known ncRNA in RNAdb and expands previous similar efforts with 6523 novel transcripts. This bioinformatic filtering of the FANTOM3 non-coding dataset has generated a lead dataset of transcripts without signs of being artefacts, providing a suitable dataset for investigation with hybridization-based techniques.

Place, publisher, year, edition, pages
2009. Vol. 94, no 3, 169-176 p.
Keyword [en]
RIKEN, FANTOM3, ncRNA, Non-coding RNA, snoRNA, EST
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-124755DOI: 10.1016/j.ygeno.2009.05.012ISI: 000269595400003PubMedID: 19505569OAI: oai:DiVA.org:uu-124755DiVA: diva2:317935
Available from: 2010-05-05 Created: 2010-05-05 Last updated: 2017-12-12Bibliographically approved

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