Review Neuroinformatics analysis of molecular expression patterns and neuron populations in gray matter regions: The rat BST as a rich exemplar Mihail Bota a , Olaf Sporns b , Larry W. Swanson a, ⁎ a Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA b Department of Psychological and Brain Sciences Programs in Neuroscience and Cognitive Science Indiana University Bloomington, IN 47405, USA ARTICLE INFO ABSTRACT Article history: Accepted 14 February 2012 Available online 22 February 2012 The rat bed nuclei of the stria terminalis (BST) is an important part of the cerebral nuclei, both structurally and functionally. However, the literature is rather scarce and more importantly, often contradictory. In this paper we review the literature related to neuron populations reported in different rat BST parts, and to a set of more than 50 expressed mol- ecules. The information related to neuron populations and molecules detected in the BST was expertly collated manually in a publicly available neuroinformatics system, the Brain Architecture Knowledge Management System (BAMS; http://brancusi.usc.edu/bkms). Using the tools implemented in BAMS, we organized the collated information, and further analyzed it statistically. The result of our analysis over the set of >50 expressed molecules confirms the BST parcellation scheme proposed by Swanson in 2004, with two exceptions. We present and discuss these results, and propose refined parcellation ventrally in the BST. We also review and discuss the presence of cholinergic neurons in the BST, and of neu- ron populations that express serotonin receptors. This review is one of the most compre- hensive for the rat BST published in the literature, and it was possible only by using neuroinformatics tools. © 2012 Elsevier B.V. All rights reserved. Keywords: Bed nuclei of stria terminalis BST Neurons types Gene expression Neuroinformatics Database BAMS Contents 1. Introduction .......................................................... 175 2. Results ............................................................. 176 2.1. BST molecular expression patterns .......................................... 177 2.2. Neuron populations .................................................. 178 2.3. Cholinergic neurons in the BST ............................................ 179 2.4. Serotonin-receptive neurons in the BST ....................................... 179 2.5. Projection neurons of the BST ............................................ 182 BRAIN RESEARCH 1450 (2012) 174 – 193 ⁎ Corresponding author at: Hedco Neuroscience Building Room 428, University of Southern California, 3641 Watt Way, Los Angeles CA 90089-2520, USA. Fax: +1 213 741 0561. E-mail address: lswanson@usc.edu (L.W. Swanson). 0006-8993/$ – see front matter © 2012 Elsevier B.V. All rights reserved. doi:10.1016/j.brainres.2012.02.034 Available online at www.sciencedirect.com www.elsevier.com/locate/brainres