Skip to main content

Transforming the understanding
and treatment of mental illnesses.

Section on Neural Gene Expression (SNGE) Section on Neural Gene Expression (SNGE)

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.

References:

  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.