Oligonucleotide microarray technology has created a small revolution in the transplant community because it has helped to decipher previously unknown molecular processes involved in allograft pathology, redefined molecular patterns of diseases that are indistinguishable at the pathological level and made possible the definition of new prognostic factors for long-term graft outcomes. However, given the tremendous complexity of the biological processes that are involved in the pathology of a transplanted organ, the interpretation of transcriptomic data can be speculative and oversimplified. Here, we discuss critical considerations regarding the nature of the object studied by cDNA microarray technology, the means by which it is observed, the interpretation of the observations, and whether the observations make sense in the context of transplant-related scientific questions. Given these limitations, we believe that global approaches based on more functional biological intermediates are necessary for a better understanding of the molecular processes that regulate the physiopathology of the transplanted organ.
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