title: A method for detecting long non-coding RNAs with tiled RNA expression microarrays.
abstract: Long non-coding ribonucleic acids (lncRNAs) have been proposed as biomarkers in prostate cancer. This paper proposes a selection method which uses data from tiled microarrays to identify relatively long regions of moderate expression independent of the microarray platform and probe design. The method is used to search for candidate long non-coding ribonucleic acids (lncRNAs) at locus 8q24 and is run on three independent experiments which all use samples from prostate cancer patients. The robustness of the method is tested by utilizing repeated copies of tiled probes. The method shows high consistency between experiments that used the same samples, but different probe layout. There also is statistically significant consistency when comparing experiments with different samples. The method selected the long non-coding ribonucleic acid PCNCR1 in all three experiments.
authors.affiliation: Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland.
authors.forename: Sigrun Helga
authors.initials: SH
authors.lastname: Lund
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Daniel Fannar
authors.initials: DF
authors.lastname: Gudbjartsson
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Thorunn
authors.initials: T
authors.lastname: Rafnar
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Asgeir
authors.initials: A
authors.lastname: Sigurdsson
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Sigurjon Axel
authors.initials: SA
authors.lastname: Gudjonsson
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Julius
authors.initials: J
authors.lastname: Gudmundsson
authors.affiliation: deCODE Genetics, Reykjavik, Iceland.
authors.forename: Kari
authors.initials: K
authors.lastname: Stefansson
authors.affiliation: Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Stefansson
mesh_terms: D000368:Aged; D063646:Carcinogenesis / Q000235:genetics / Q000378:metabolism; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D003198:Computer Simulation; D006801:Humans; D008297:Male; D008875:Middle Aged; D008957:Models, Genetic; D009010:Monte Carlo Method; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding