brainexpressed

Brainexpressed is a term used in genomics to describe genes whose expression is enriched in brain tissue compared with non-brain tissues. In practice, a brainexpressed gene shows higher transcriptional activity in one or more brain regions and, in many cases, relative tissue specificity. The concept is used to distinguish genes that contribute to brain function from those with widespread or non-neural roles.

Researchers identify brainexpressed genes by comparing transcriptomic data across tissues using resources such as BrainSpan, GTEx, or single-cell RNA sequencing atlases. Expression levels are often quantified as TPM or FPKM, and brain enrichment is assessed with fold-change thresholds and statistical testing. Common criteria include a higher mean brain expression relative to non-brain tissues, a significant adjusted p-value, and a measure of brain specificity such as a tissue specificity index or tau score. Results can be reported at the level of whole brain regions or at specific cell types.

Brainexpressed genes tend to encode proteins involved in neuronal signaling, synaptic structure, neurodevelopment, and glial function. They are useful for studying brain development, evolution, and disease. However, the label can be affected by sampling bias, developmental stage, and cellular composition of brain tissue; thus, brain-specific expression may reflect particular cell types rather than universal brain activity.

Applications include identifying candidate biomarkers for neurological disorders, prioritizing therapeutic targets for CNS conditions, and informing studies of brain evolution and function. Limitations include variability across datasets and the challenge of distinguishing cell-type–specific expression within heterogeneous brain tissue.

See also: brain-specific gene expression, transcriptomics, GTEx, BrainSpan.