Question: Why does the Gene Table in Loupe Browser highlight up-regulated genes by default?
Answer: Up-regulated genes are more straightforward to interpret than down-regulated genes when analyzing single-cell gene expression data.
Since only a fraction of expressed transcripts can be detected in most single gene expression assays, a gene may have zero or low UMI counts for reasons other than biology i.e. the absence of evidence is not evidence of absence.
Displaying up-regulated genes is also more consistent with how clusters are typically annotated (using enriched expression or up-regulation of known cell-type specific markers).