NeuroExpresso: A cross-laboratory database of brain cell-type expression profiles with applications to marker gene identification and bulk brain tissue transcriptome interpretation

The identification of cell type marker genes, genes highly enriched in specific cell types, plays an important role in the study of the nervous system. In particular, marker genes can be used to identify cell types to enable studies of their properties. Marker genes can also aid the interpretation of bulk tissue expression profiles by revealing cell type specific changes. We assembled a database, NeuroExpresso, of publicly available mouse brain cell type-specific gene expression datasets. We then used stringent criteria to select marker genes highly expressed in individual cell types. We found a substantial number of novel markers previously unknown in the literature and validated a subset of them using in silico analyses and in situ hybridization. We next demonstrate the use of marker genes in analysis of whole tissue data by summarizing their expression into “cell type profiles” that can be thought of as surrogates for the relative abundance of the cell types across the samples studied. Further analysis of our cell type-specific expression database confirms some recent findings about brain cell types along with revealing novel properties, such as Ddc expression in oligodendrocytes. To facilitate further use of this expanding database, we provide a user-friendly web interface for the visualization of expression data. Significance Statement Cell type markers are powerful tools in the study of the nervous system that help reveal properties of cell types and acquire additional information from large scale expression experiments. Despite their usefulness in the field, known marker genes for brain cell types are few in number. We present NeuroExpresso, a database of brain cell type specific gene expression profiles, and demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. The database will prove itself as a useful resource for researchers aiming to reveal novel properties of the cell types and aid both laboratory and computational scientists to unravel the cell type specific components of brain disorders.