# Comparing cross-organ gene expression levels: How much, and where are genes expressed? **URL:** \ **Category:** Science\ **Tags:** brain, transcriptomics, human, how-to, comparative-bio\ **Created:** [September 11, 2019, 8:34pm UTC](https://community.brain-map.org/t/comparing-cross-organ-gene-expression-levels-how-much-and-where-are-genes-expressed/267 "2019-09-11T20:34:59Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![brain](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/brain/32/38_2.png) [@brain](https://community.brain-map.org/u/brain)\ **Post date:** [September 11, 2019, 8:34pm UTC](https://community.brain-map.org/t/comparing-cross-organ-gene-expression-levels-how-much-and-where-are-genes-expressed/267/1 "2019-09-11T20:34:59Z")
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](https://www.ebi.ac.uk/gxa/home) 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](http://www.informatics.jax.org/expression.shtml) (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)](https://www.nature.com/articles/sdata2017185) presents an analysis of comprehensive RNA-Seq datasets across the same 13 tissues for mouse and rat. For human, the [Human Cell Atlas](https://www.humancellatlas.org/) project and [Human BioMolecular Atlas Program](https://commonfund.nih.gov/hubmap) (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. ---
**Author:** ![trygveb](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/trygveb/32/2304_2.png) [@trygveb](https://community.brain-map.org/u/trygveb)\ **Post date:** [September 11, 2019, 9:15pm UTC](https://community.brain-map.org/t/comparing-cross-organ-gene-expression-levels-how-much-and-where-are-genes-expressed/267/2 "2019-09-11T21:15:50Z")
[GTEx](https://gtexportal.org/home/tissueSummaryPage) has standardized expression measured from 54 tissues across hundreds of human donors. ---
**Author:** ![lucasg](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lucasg/32/35_2.png) [@lucasg](https://community.brain-map.org/u/lucasg)\ **Post date:** [September 11, 2019, 9:57pm UTC](https://community.brain-map.org/t/comparing-cross-organ-gene-expression-levels-how-much-and-where-are-genes-expressed/267/3 "2019-09-11T21:57:13Z")
This publication is the source for one of the main datasets displayed in the NCBI Gene tool for tissue specificity: > > > Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body. This includes a supplementary table with gene expression values from RNA-seq of many human tissues.