One of the core aims of differential expression analysis is to understand what is regulating any differentially expressed genes. One method to help determine this is Upstream Regulator Analysis (URA). In URA a predefined database of upstream regulator genes alongside the genes that each regulates, and the typical direction of that regulation (e.g. TNFA upregulates PCP2 and downregulated TNFIAP3) is supplied, alongside a list of observed differential expression fold changes. The upstream regulator algorithm then determines for each upstream regulator how closely the observed pattern of differential expression matches the expected pattern. Enrichment of an activated or inhibited regulator is indicated as a z-score.
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Here we provide boxplots showing the ten showing ten most enriched, activated and inhibited upstream regulators, and the expression values for the genes within each upstream regulators. The expression values are given as z-scores. As well as provide a useful insight into the types of regulators that may be controlling the differential biology this also shows how convincing the evidence is, and which individual genes are most affected.
