Critical evaluation of the FANTOM3 non-coding RNA transcripts

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Critical evaluation of the FANTOM3 non-coding RNA transcripts. / Nordström, Karl J V; Mirza, Majd A I; Almén, Markus Sällman; Gloriam, David Erik Immanuel; Fredriksson, Robert; Schiöth, Helgi B.

In: Genomics, Vol. 94, No. 3, 2009, p. 169-176.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Nordström, KJV, Mirza, MAI, Almén, MS, Gloriam, DEI, Fredriksson, R & Schiöth, HB 2009, 'Critical evaluation of the FANTOM3 non-coding RNA transcripts', Genomics, vol. 94, no. 3, pp. 169-176. https://doi.org/10.1016/j.ygeno.2009.05.012

APA

Nordström, K. J. V., Mirza, M. A. I., Almén, M. S., Gloriam, D. E. I., Fredriksson, R., & Schiöth, H. B. (2009). Critical evaluation of the FANTOM3 non-coding RNA transcripts. Genomics, 94(3), 169-176. https://doi.org/10.1016/j.ygeno.2009.05.012

Vancouver

Nordström KJV, Mirza MAI, Almén MS, Gloriam DEI, Fredriksson R, Schiöth HB. Critical evaluation of the FANTOM3 non-coding RNA transcripts. Genomics. 2009;94(3):169-176. https://doi.org/10.1016/j.ygeno.2009.05.012

Author

Nordström, Karl J V ; Mirza, Majd A I ; Almén, Markus Sällman ; Gloriam, David Erik Immanuel ; Fredriksson, Robert ; Schiöth, Helgi B. / Critical evaluation of the FANTOM3 non-coding RNA transcripts. In: Genomics. 2009 ; Vol. 94, No. 3. pp. 169-176.

Bibtex

@article{ad0968009bcd11df928f000ea68e967b,
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.",
keywords = "The Faculty of Pharmaceutical Sciences",
author = "Nordstr{\"o}m, {Karl J V} and Mirza, {Majd A I} and Alm{\'e}n, {Markus S{\"a}llman} and Gloriam, {David Erik Immanuel} and Robert Fredriksson and Schi{\"o}th, {Helgi B}",
note = "Keywords: Computational Biology; Databases, Genetic; EST; Expressed Sequence Tags; FANTOM3; Genome, Human; Humans; Introns; ncRNA; Non-coding RNA; Proteins; RIKEN; RNA, Messenger; RNA, Untranslated; Sequence Analysis, RNA; snoRNA; Transcription, Genetic",
year = "2009",
doi = "10.1016/j.ygeno.2009.05.012",
language = "English",
volume = "94",
pages = "169--176",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press",
number = "3",

}

RIS

TY - JOUR

T1 - Critical evaluation of the FANTOM3 non-coding RNA transcripts

AU - Nordström, Karl J V

AU - Mirza, Majd A I

AU - Almén, Markus Sällman

AU - Gloriam, David Erik Immanuel

AU - Fredriksson, Robert

AU - Schiöth, Helgi B

N1 - Keywords: Computational Biology; Databases, Genetic; EST; Expressed Sequence Tags; FANTOM3; Genome, Human; Humans; Introns; ncRNA; Non-coding RNA; Proteins; RIKEN; RNA, Messenger; RNA, Untranslated; Sequence Analysis, RNA; snoRNA; Transcription, Genetic

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

KW - The Faculty of Pharmaceutical Sciences

U2 - 10.1016/j.ygeno.2009.05.012

DO - 10.1016/j.ygeno.2009.05.012

M3 - Journal article

VL - 94

SP - 169

EP - 176

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 3

ER -

ID: 21087519