Critical evaluation of the FANTOM3 non-coding RNA transcripts

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• 作者：Karl J.V. Nordströ ; m ; Majd A.I. Mirza ; Markus S&#xe4 ; llman Alm&#xe9 ; n ; David E. Gloriam ; Robert Fredriksson ; Helgi B. Schiö ; th
• 关键词：RIKEN ; FANTOM3 ; ncRNA ; Non-coding RNA ; snoRNA ; EST
• 刊名：Genomics
• 出版年：2009
• 出版时间：September 2009
• 年：2009
• 卷：94
• 期：3
• 页码：169-176
• 全文大小：322 K

文摘

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.