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For those studies seeking to find the mechanisms/genes dysregulated in the tissue of interest, the large majority have been structured very similarly: a direct comparison is made between expression profiling of peripheral blood and the specific tissue where the disease is known to develop.
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Genes co-expressed with DCN were identified by pairwise correlation analysis between expression profiles of DCN and each other gene measured by the Affymetrix microarrays, using the Pearson's rank correlation coefficient.
We also calculated the correlation between expression profiles of TUs and erythromycin production rate respectively.
We observed a good similarity between expression profiles of the duplicate clones of each candidate gene.
Briefly, Gemma uses a threshold of 0.5% on the correlation between expression profiles of genes to determine coexpression, or a p-value from the Fisher transformed correlations, whichever is more stringent [34].
Indeed, our analysis of genes regulated in iTregs and in Teffs at different time points revealed a strong overlap at the beginning of the development with increasing differences between expression profiles of developing iTregs and Teffs up to the most pronounced differences between mature iTregs and Teffs.
These data were further substantiated by a principle component analysis (PCA), using a mean centering and scaling, which showed a similar correlation between expression profiles of the different organs, albeit an increased distance was observed between the gonads and brains (Fig. S4).
Divergence between expression profiles of homologous genes is often calculated with Pearson's or Euclidean distance.
Similarities between expression profiles of AHL genes were calculated using Pearson Correlation method (www.genevestigator.com ) [ 67 ].
Similarities between expression profiles of AHL genes were calculated using Manhattan Distance method (www.genevestigator.com ) [ 67 ].
In addition, we found stronger correlation between expression profiles of orthologous tissues than non-orthologous tissues.
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