title: Critical evaluation of the FANTOM3 non-coding RNA transcripts.
abstract: 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.
authors.affiliation: Department of Neuroscience, Uppsala University, Sweden. karl.nordstrom@neuro.uu.se
authors.forename: Karl J V
authors.initials: KJ
authors.lastname: Nordström
authors.forename: Majd A I
authors.initials: MA
authors.lastname: Mirza
authors.forename: Markus Sällman
authors.initials: MS
authors.lastname: Almén
authors.forename: David E
authors.initials: DE
authors.lastname: Gloriam
authors.forename: Robert
authors.initials: R
authors.lastname: Fredriksson
authors.forename: Helgi B
authors.initials: HB
authors.lastname: Schiöth
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015894:Genome, Human; D006801:Humans; D007438:Introns / Q000235:genetics; D011506:Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D011506:Proteins; D012333:RNA, Messenger; D022661:RNA, Untranslated