Comment on " 'Stemness': Transcriptional Profiling of Embryonic and Adult Stem Cells" and "A Stem Cell Molecular Signature" (II)

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Considering the virtual identity of experimental material and methods used in the two reports, this degree of overlap hardly justifies the ambitious statements cited above. It seems that “stemness” genes are elusive and cannot be readily identified by the approaches presented in these two papers. It has been suggested (3) that “important differences in methodology” could explain the almost total lack of overlap—namely, that Ivanova et al. (2) probed the entire Affymetrix U74 set (36,000 mouse genes and EST clusters), whereas Ramalho-Santos et al. (1) probed only U74A (12,000 genes and EST clusters). This difference cannot be used as an explanation, however, because logically, Ivanova et al. should have found every gene and EST that Ramahlo-Santos et al. detected and, indeed, many more. In addition, out of the 283 “stemness” genes listed by Ivanova et al., 82 are present on the U74A array and should all have been found by Ramalho-Santos et al.; instead, they found only six.

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