A method for detecting long non-coding RNAs with tiled RNA expression microarrays

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 metho...

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Bibliographic Details
Published inPloS one Vol. 9; no. 6; p. e99899
Main Authors Lund, Sigrun Helga, Gudbjartsson, Daniel Fannar, Rafnar, Thorunn, Sigurdsson, Asgeir, Gudjonsson, Sigurjon Axel, Gudmundsson, Julius, Stefansson, Kari, Stefansson, Gunnar
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 17.06.2014
Public Library of Science (PLoS)
Subjects
Acids
Aged
Arrays
Bioinformatics
Biology and Life Sciences
Biomarkers
Cancer
Carcinogenesis - genetics
Carcinogenesis - metabolism
Chromosome 8
Chromosomes, Human, Pair 8 - genetics
Computer Simulation
Consistency
Data analysis
DNA probes
Experiments
Gene expression
Genomes
Genomics
Humans
Male
Medicine and Health Sciences
Methods
Middle Aged
Models, Genetic
Monte Carlo Method
Non-coding RNA
Oligonucleotide Array Sequence Analysis
Physical Sciences
Prostate cancer
Prostatic Neoplasms - genetics
Prostatic Neoplasms - metabolism
Proteins
Quality control
Ribonucleic acid
RNA
RNA, Long Noncoding - genetics
RNA, Long Noncoding - metabolism
Statistical analysis
Statistical methods
Studies
Transcriptome
Trends
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Summary: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.
Bibliography:Conceived and designed the experiments: SHL GS JG TR SAG KS. Performed the experiments: AS. Analyzed the data: SHL DFG GS. Contributed reagents/materials/analysis tools: AS SAG SHL. Wrote the paper: SHL TR GS.
Competing Interests: Daniel Fannar Gudbjartsson, Thorunn Rafnar, Asgeir Sigurdsson, Sigurjon Axel Gudjonsson, Julius Gudmundsson and Kari Stefansson are employed by a commercial company, deCODE Genetics. This does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0099899