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raw data produced by different studies was estimated using Integrated Correlation Analysis. This method produces a general coefficient called Integrated Correlation Coefficient, with similar interpretations as the Pearson correlation coefficient, which represents agreement between studies. Additionally, ICC can be used to eliminate background noise prior to the analysis, excluding genes that exhibit incoherent behavior across studies. For 14483 probe-sets that passed the first-step filtering and were then common among the 5 studies, the ICC was calculated as 0.406. When genes with poor coherent behavior were filtered out, an improvement on the ICC to 0.569 was observed. The resulting 10862 probe sets were used for downstream analysis. Psoriasis MAD Transcriptome Model Specification A random effect meta-analysis model was used to analyze the expression differences between LS and NL samples. The choice of using a random or a fixed effect meta-analysis was based on the comparison between sample quantiles of Cochran’s Q and the quantiles of its theoretical distribution as suggested by Choi PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22212322 et al.. The QQplot shows a substantial deviation in Cochran’s Q from the desired distribution indicating that a random effect model is more appropriate. Comparing the standardized overall effect estimates from the random effect meta-analysis model to a standard normal distribution shows that those estimates do not deviate dramatically from normality. The MAD Transcriptome in Psoriasis The meta-analysis of 5 studies allowed us to estimate the overall difference in expression values between LS and NL samples across studies. Using FDR,0.05 and FCH.2, which were the same cut-offs for all the published studies, we identified 854 up-regulated and 550 down-regulated probe-sets representing 677 and 443 known unique genes, respectively. We refer to this transcriptome as MAD-5. A microarray meta-analysis is restricted to the universe of genes commonly present on each chip platform used for sample hybridization. The hgu133plus2 chips contain more than twice the number of probe-sets than the hgu133a2 chips, representing 7315 genes whose effect size cannot therefore be assessed by MAD-5, and which may be biologically relevant. Therefore the same analysis was carried out considering the 163 LS and NL pairs from the 3 studies that used hgu133plus2 chips. Using 25% cutoff for coherence scores, 24375 probe sets were considered for downstream analysis. The transcriptome for 133plus2 encompassed 1412 up-regulated and 959 down-regulated probe-sets representing 1084 and 748 genes, Lonafarnib site respectively, a list considerably larger than the MAD-5 transcriptome. The intersection of DEGs reported by the 5 individual studies consisted of 78 up- and 22 down-regulated genes. However, the global psoriasis transcriptome obtained by the MAD-5 is much larger than this intersection and successfully identified those 100 genes. When only hgu133plus2-studies were considered, 340 up- and 190 down-regulated genes were in the intersection, and all but 4 genes were identified by the meta-analysis. A simplified heat-map is presented in 3 Psoriasis MAD Transcriptome showing how the DEGs in each individual study relate with those identified by the meta-analyses. The 4 genes from the intersection that were not identified by the MAD-3 were IDA, LEPR, MYOCD and TYMP. In the metaanalysis several factors intervene in the estimation of the overall summary statistics for each gene: the log-fold change, its corre

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