Project description:This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison
Project description:This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison Genomic response one day post traumatic injury was compared between patients having early or late respiratory recovery
Project description:Hairy vetch (Vicia villosa Roth) is recognized as a beneficial winter cover crop in the Midwestern U.S. DNA microarrays are used for assessing gene expression significance. The objective of the study was to identify a set of genes expressed in hairy vetch, that could be further analyzed for their potential in improving the crop. The RNA of four targets (soybean (Glycine max), hairy vetch, Vicia pannonica PI 170008, and Vicia pannonica PI 515988) were purified, labeled, and hybridized to 142 cDNA clones of biotic stress genes and gene sequences of soybean that were robotically spotted onto aminosilicated slides with duplicate spots and three arrays per slide. The microarray experiments were completed in a reference design experiment incorporating a two-dye system. The data were analyzed using the individual fluorescence intensities to fit two statistical models in a mixed model analysis of variance. In this analysis, systematic error effects were observed to account for 24% of the total variation. The use of a Bonferroni adjusted significance threshold allowed for adequate control over the number of falsely identified significant genes showing expression in the different target comparisons. We observed that 64 of the 142 gene sequences (45%) were differentially expressed in at least one of the target comparisons. Two of these expressed genes in hairy vetch encoded for a cold tolerance indicator, proline, and two other gene sequences encode for stress tolerance indicators, myo-inositol and calmodulin. A soybean cDNA microarray was used effectively to differentiate gene expression in hairy vetch. Keywords: comparative genomic hybridization (cross-species)
Project description:We propose a method to compare the location and variability of gene ex-pression between two groups of microarrays using a permutation test based on the pairwise distance between microarrays. The microarrays could be samples from distinct clinical or biological populations or microarrays prepared at two different levels of an experimental factor. For these tests the entire microarray or some pre-specifed subset of genes, not the individual gene, is the unit of analysis. We apply this method to compare results from two dfferent protocols for preparing labeled targets for microarray hybridization and their subsequent gene expression analysis. Keywords: Comparative genomic expression
Project description:circRNA microarrays were performed with 2 pairs of tongue squamous cell carcinoma and their matched adjacent tissues. The statistical significance of the difference was estimated by t-test. circRNAs having fold changes 1.5 and p-values 0.05 are selected as the significantly differentially expressed. The data from microarray indicated that there were 54 upregulated and 70 downregulated circRNAs in TSCC tissues.
Project description:A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads. Statistical analysis with SAM (Significance Analysis of Microarray) didn’t identify any difference in expression patterns between the two groups. Samples were then employed as biological replicates to determine array-to-array reproducibility, the degree of mutual agreement among replicates was estimated using Pearson correlation coefficients on the entire set of expression values. For all pairs of experiments correlation coefficients were always significant (p-value <0.01) and never less than 0.99.
Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues.
