With the completion of the sequencing of the human genome and of the genomes of other model organisms, there is a need to understand the function of each of those genes. One way to do this is to integrate this genome-wide information with patterns of gene expression, and, with this in mind, several projects have been initiated to examine global gene expression patterns during development and in the adult. The mammalian brain presents a particular challenge for an undertaking of this nature owing to the intricacies of its structure and the complexity of its gene expression patterns. In the early 1990s, the US National Institutes of Health launched what became the Brain Mapping Anatomy Project (BMAP), which had the ambitious goal of producing a systematic, three-dimensional map of gene expression in the mammalian brain(the brains of human, monkey and mouse) for all of the genes in the genome. The Allen Institute for Brain Science, founded in 2003, is devoted to this goal, and in 2006 it completed a comprehensive gene expression map for the brain of the C57BL/6J male mouse, using brains from 8-week-old mice prepared as unfixed, fresh-frozen tissue. This map is freely available online as the Allen Brain Atlas (ABA, www.brain-map.org),and the results were published in 2007(Lein et al., 2007). Anyone who has used the ABA can attest to its usefulness, as well as its comprehensive nature; it is an indispensable tool for anyone interested in the molecular aspects of brain organization and function.FIG1
An online repository of information is needed for all of the data in the ABA, but the resolution of images is not always satisfactory and can be below that of the best and most useful atlases. For this reason, the Allen Institute has now published the Allen Reference Atlas (ARA) in book form. The goal of this book is to create a solid, detailed neuroanatomical reference book that integrates with the ABA online. In the book, which compares favorably with the best anatomical atlases, there are 132 fully annotated,high-resolution coronal sections evenly spaced at 100 μm intervals, as well 21 representative sagittal sections spaced at 200 μm of the 8-week-old C57BL/6J male mouse. These images are also reproduced online as full-color,high-resolution, web-based digital brain atlases. Brain regions are annotated using a systematic taxonomy of mouse brain structures, resulting in annotation that is as good as in any mouse brain atlas. The expression data are fully integrated into this annotated neuroanatomical atlas, allowing the ABA online to function as a detailed searchable gene expression database. In addition,the book has an introduction of 25 pages that describes the ABA and ARA,including their philosophy and approach to the problem, providing material that is not available online.
The best recommendation for this book is that it was always located either open by the microscopes or at someone's desk
The Allen Brain Institute has of course succeeded magnificently in their goal to integrate the detailed ABA and ARA, and have given detailed attention to the expression patterns and neuroanatomy. There is no doubt that this will be the definitive atlas for gene expression in the mouse brain. It will be highly useful to anyone wanting to know the pattern of expression of a single gene or of groups of genes in the adult brain, or which genes are expressed in a particular structure. Unfortunately, there is no atlas for different developmental time points in the brain, but perhaps this will be a future project. I certainly hope that it is in the planning stages. There are currently two other projects at the ABA, which provide atlases for the adult mouse spinal cord and human cortex online, and a future project will examine gene expression during sleep deprivation and sleep states in the mouse brain. Given the level of detail in the current ABA and ARA on the mouse brain, these new resources will surely be equally indispensable.
Why does one need a book when the atlases are available online? In the introduction to the print version of the ARA, the author suggests that it could be used with the ABA, similar to the way one uses an anatomy reference book while looking down a microscope. For studying the intricacies of development or brain structure and function in histological sections, an anatomically detailed and high-resolution atlas is essential to orient the investigator to what he or she is seeing online or under the microscope. This seems to me the optimal way to visualize and conceptualize the online expression patterns, given that I have used books in this way in the past.
You may think that this is an old-fashioned approach. However, I left the book for a few months in my lab and asked my students and fellows to let me know what they thought of it. They were unanimous in thinking that it was very useful. Probably the best recommendation for this book is that it was always located either open by the microscopes or at someone's desk, and after exposure to my lab members, it was soon well worn. I cannot think of a better recommendation.