Gene expression in the brain has the highest complexity. There are few websites with the gene expression data such as Allen Brain Atlas, GenePaint, Gensat, Emage and EurExpress. These databases contain gene expression information derived mostly from in situ hybridization carried out in an institution or in a specific laboratory. There is vast amount of microarray derived gene expression data deposited at Gene Expression Omnibus (GEO) ArrayExpress and other data warehouses. Molecularbrain is an attempt to complement existing gene expression databases by deriving gene expression information from microarray experiments. Here gene expression data from various brain regions can be visualized side by side in a graphical form.

Mouse transcriptome database provides relative signal values for expression for all genes investigated in ten different brain regions of mouse investigated by microarray technique. As C57BL has been the most used mouse strain, this database initially provides expression information for different brain regions of this strain. Other strains will be added later. Only the processed data from experiments were obtained from GSE files of GEO and collated as described HERE. Data from developmental stages, treated and disease samples were excluded.

The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Expression information about any gene from eleven brain regions can be obtained as a histogram. Because of lab to lab variation in the absolute values, the processed signals have been normalized to beta2microglobulin expression set at 100.

Gene information along with their expression values can also be accessed from the alphabetical list of gene symbols on the footer. Information about the protocol and GEO samples used here are also available on each gene page.

From the expression display page, one can also access other relevant information about that specific gene/protein such as its expression (as reported in databases based on in situ hybridization, SAGE, EST), gene ontology, pathways, networks and protein and nucleotide sequences by using the pull down menu. There are also links to protocols for data analysis.

Any comments and suggestions for improvement and collaboration will be gladly appreciated. Contact info is present on each page.

Babru Samal