Abstract: Integrated understanding of complexity of brain structure and gene expression is crucial for molecular research into neural organization and function.Here I would introduce a novel framework, Transcriptome Tomography, for spatially integrating comprehensive endogenous gene expression withinan isotropic anatomical context of the web-accessible standard space for brain-atlas databases, e.g. Waxholm Space. Using this rapid and unbiased3D mapping technique, in the first instance, we generated a dataset of transcriptome maps covering the whole mouse brain and validated themagainst existing datasets. Then, we used an informatics approach to identify the combinatorial gene expression as a broad co-expression network. The gene network links followed an inverse-power law and were rich in functional interaction. To demonstrate the relevance of the finding, wemined Huntington’s disease gene (Htt) and found a novel disease-related co-expression network containing genes potentially co-functioning with Httand modulating the disease specific differential vulnerability in brain regions.