Málstofa í stærðfræði
Fyrirlesari: Sigrún Helga Lund, Háskóli Íslands
Titill: Multiple spots with the same probe on tiled RNA expression microarrays
Staðsetning: V-157, VRII
Tími: Mánudagur 10. nóvember, frá 15:00 til 16:00.
Ágrip:
Tiled microarrays are a technology to target non-coding RNAs. In this thesis, custom arrays are designed with the same probe at multiple locations. This allows measuring sources of errors in microarray data that are otherwise neglected, as well as measuring the consistency of selection methods. The analyses performed in this thesis can broadly be split in two categories; analysing sources of variation in microarray data and developing selection methods for targeting expressed and differentially expressed regions. These analyses are the substance of the four papers: Paper I estimates the difference in signal intensities both within and between probe pairs that contain a Single Nucleotide Polymorphism and differ only by the varying allele. The majority of probe-pairs with sufficiently high expression have significant differences in expression levels within the pair that is consistent with the genotype. By using the expression level of the probe within the probe-pair that has the higher value, one receives more accurate estimates. Paper II shows that most RNA sequences are pairwise significantly differently expressed, including randomly generated ones. A search for sequences with expression levels which are significantly different from the population of random ones is therefore proposed. The analysis of within-array replicates indicates that within-array variability can be considerable and can be reduced by replicating probes within the array. Paper III proposes a selection method to identify relatively long regions of moderate expression. The method is used to search for candidate long non-coding RNAs (lncRNAs) at locus 8q24.2 and is run on three independent experiments. The method shows high consistency between experiments that used the same samples, but different probe layout. There is statistically significant consistency between experiments on different samples. Paper IV evaluates the TileShuffle method as a method of finding lncRNAs at 8q24.2. The method is run on three microarrays which all contained the same sample and repeated copies of tiled probes. Monte Carlo simulations showed poor consistency in areas selected between arrays. A crude application of the method can result in most of the region being selected. This thesis shows how repeating the same probe on multiple spots on a microarray can greatly improve accuracy of expression estimates; new methods for locating expressed regions can be applied that show greater consistency than conventional methods. Finally, guidelines for design of tiled microarray experiments are proposed that may be beneficial for all users of tiled microarray experiments.Math Colloquium
Speaker: Sigrún Helga Lund, University of Iceland
Title: Multiple spots with the same probe on tiled RNA expression microarrays
Location: V-157, VRII
Time: Monday, November 10 at 15:00-16:00.
Abstract:
Tiled microarrays are a technology to target non-coding RNAs. In this thesis, custom arrays are designed with the same probe at multiple locations. This allows measuring sources of errors in microarray data that are otherwise neglected, as well as measuring the consistency of selection methods. The analyses performed in this thesis can broadly be split in two categories; analysing sources of variation in microarray data and developing selection methods for targeting expressed and differentially expressed regions. These analyses are the substance of the four papers: Paper I estimates the difference in signal intensities both within and between probe pairs that contain a Single Nucleotide Polymorphism and differ only by the varying allele. The majority of probe-pairs with sufficiently high expression have significant differences in expression levels within the pair that is consistent with the genotype. By using the expression level of the probe within the probe-pair that has the higher value, one receives more accurate estimates. Paper II shows that most RNA sequences are pairwise significantly differently expressed, including randomly generated ones. A search for sequences with expression levels which are significantly different from the population of random ones is therefore proposed. The analysis of within-array replicates indicates that within-array variability can be considerable and can be reduced by replicating probes within the array. Paper III proposes a selection method to identify relatively long regions of moderate expression. The method is used to search for candidate long non-coding RNAs (lncRNAs) at locus 8q24.2 and is run on three independent experiments. The method shows high consistency between experiments that used the same samples, but different probe layout. There is statistically significant consistency between experiments on different samples. Paper IV evaluates the TileShuffle method as a method of finding lncRNAs at 8q24.2. The method is run on three microarrays which all contained the same sample and repeated copies of tiled probes. Monte Carlo simulations showed poor consistency in areas selected between arrays. A crude application of the method can result in most of the region being selected. This thesis shows how repeating the same probe on multiple spots on a microarray can greatly improve accuracy of expression estimates; new methods for locating expressed regions can be applied that show greater consistency than conventional methods. Finally, guidelines for design of tiled microarray experiments are proposed that may be beneficial for all users of tiled microarray experiments.