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5 μm-thick sections of formalin-fixed, paraffin-embedded tissue microarrays were de-paraffinized and rehydrated.

Tissue microarray slides were de-paraffinized in xylene and re-hydrated through standard protocols.

Tissue microarrays were constructed as described previously (de Graeff et al, 2006).

Microarrays were obtained from the Service de Genomique Fonctionnelle (CEA, Evry, France).

Microarrays were hybridized and scanned at the Institut de Recerca Hospital Universitari Vall d'Hebron (Barcelona, Spain) following Affymetrix standard protocols.

One of the many advantages of RNA-Seq over microarrays is that it enables de novo analysis of transcripts, including novel transcripts.

Fifty microarrays were included in our previously published study and publicly available at www.genomika.pl/thyroidcancer (Jarzab et al. 2005 ); 40 microarrays were from de novo studies.

All microarrays were hybridized together.

Only "present" probes in microarrays were included.

Three microarrays were performed for each probe.

Microarrays were constructed as previously described [47].