Apr 25, 2020

Overcoming bias in gene-set enrichment analyses of brain-wide transcriptomic data

BioRxiv : the Preprint Server for Biology
Ben D. FulcherA. Fornito


The recent availability of whole-brain atlases of gene expression, which quantify the transcriptional activity of thousands of genes across many different brain regions, has opened new opportunities to understand how gene-expression patterns relate to spatially varying properties of brain structure and function. To aid interpretation of a given neural phenotype, gene-set enrichment analysis (GSEA) has become a standard statistical methodology to identify functionally related groups of genes, annotated using systems such as the Gene Ontology (GO), that are associated with a given phenotype. While GSEA has identified functional groups of genes related to diverse aspects of brain structure and function in mouse and human, here we show that these results are affected by substantial statistical biases. Quantifying the false-positive rates of individual GO categories across an ensemble of completely random phenotypic spatial maps, we found an average 875-fold inflation of significant findings relative to expectation in mouse, and a 582-fold inflation in human, with some categories being judged as significant for over 20% of random phenotypes. Concerningly, the probability of a GO category being reported as significant in the extant l...Continue Reading

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