Comparing cross-organ gene expression levels: How much, and where are genes expressed?

We received a query from a scientist who seeks a list of CNS-specific genes, loosely defined as genes that are differentially expressed in the brain as compared to other tissues or organs in the body. This is a surprisingly complex question, as it requires a system-by-system integration of gene expression data modalities that are normalized for accurate quantitative comparison. The level of resolution is also a key question – would gene expression normalized to the level of an organ be sufficient? Probably not - but perhaps the cellular level is too detailed. It depends on the broader use of this information, and also what type of gene expression measurement is relevant for the analysis – perhaps protein detection, or mRNA, or even evaluation of chromosomal state.

While we are unaware of a single, broad reference resource, there are resources available that may be useful. EMBL-EBI’s Gene Expression Atlas is a clearinghouse of transcriptional data collected from, at the time of this writing: 62 species, 3,588 studies, 114,907 assays. The quality of the data for practical use in guiding experimental design will depend on which datasets are evaluated, and whether the relevant controls and standards are cross-comparable.

In the mouse, the searchable Mouse Genome Database (MGD) provides detailed gene expression information across multiple datasets, data modalities and metadata such as age.

Considering the question for both mouse and rat, a publication by Sollner, et al. (2017) presents an analysis of comprehensive RNA-Seq datasets across the same 13 tissues for mouse and rat.

For human, the Human Cell Atlas project and Human BioMolecular Atlas Program (HuBMAP) are emerging initiatives that seek to establish ground truth, whole-body transcriptional profiling data repositories that will certainly be valuable to the research community.

What else is out there? Input on other resources that may be useful for transcriptional comparisons is welcome.

GTEx has standardized expression measured from 54 tissues across hundreds of human donors.


This publication is the source for one of the main datasets displayed in the NCBI Gene tool for tissue specificity:

This includes a supplementary table with gene expression values from RNA-seq of many human tissues.