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Section on Neural Gene Expression

Comments on Allen Brain Atlas

Comments on Allen Brain Atlas

Allen Brain Atlas is a great resource but use thoughtfully

The genome-wide atlas of gene expression in the adult mouse brain 1  is without doubt a valuable resource for the neuroscience community. A great deal of care and effort clearly has been devoted to this project. However, I believe a word of caution is warranted with regard to the specificity of probes used. Although the Methods state that probes "were designed against unique regions of transcripts to avoid cross-reactivity," this is not always the case. Given our interest in neurohormone oxytocin (Oxt), we examined the probe used to map the transcript encoding Oxt 2 and saw that it has significant identity with the transcript encoding vasopressin (Avp). In fact, there is no difference in base sequence over a stretch of 127bp and a difference at only three positions over 182bp.

This accounts for the atlas's inaccurate display of hybridization to Oxt mRNA in the suprachiasmatic nucleus 3 where only Avp, but not Oxt, is in fact expressed4. There may be other similar cases within related families of genes so one would be wise to evaluate ("BLAST", ref. 5  ) any probe of interest before accepting on faith the distribution as shown in the atlas.


  1. Lein, E.S. et al. The genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176 (2007).
  2. Allen Institute for Brain Science oxytocin probe sequence. (link inactive)
  3. Allen Institute for Brain Science image of oxytocin in the SCN. (link inactive)
  4. Castel, M. & Morris, J.F. The neurophysin-containing innervation of the forebrain of the mouse. Neuroscience 24, 937-966 (1988)
  5. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990)

Note: The Oxt probe was corrected with the dataset release of 2/26/08.