Differentially expression profiling in Hashimoto's thyroiditis (HT), papillary thyroid carcinoma (PTC) with HT in background, PTC without HT in background, micro PTC (mPTC), and three normal thyroid samples (TN).

Experiment: Establishment of expression profiles in HT, PTC with HT, PTC without HT, and mPTC in comparison to TN samples. TN samples were downloaded as CEL files from the repository of the microarray vendor. Biostatistical analysis focussed in first instance on identifying genes and biofunctions related to HT and PTC with HT. We extracted RNA from tumor specimens and RNA with an RIN > 5 (Bioanalyzer, Agilent) or, in exceptional cases, RNA assessed by gel electrophoresis, was processed using the recommended processing kits and hybridized to Affymetrix Human Gene 1.0 ST arrays. Three normal tissue samples were downloaded as CEL files from the data resource center of the vendor (https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/microarray-analysis-sample-data/gene-st-array-data-set.html): TisMap_Thyroid_01_v1_WTGene1, TisMap_Thyroid_02_v1_WTGene1, TisMap_Thyroid_03_v1_WTGene1. All CEL files were RMA normalized and ANOVA was applied to generate differentially expressed probe sets. Differentially expressed genes that were significantly associated with one or more disease categories were subjected to biofunctional analysis. The renormalized cases from GSE54958 are included in the current study.