When using tools such as chromvar to evaluate the motif activity in scATAC-seq data, I noticed a frequent claim that there should be a negative correlation between the expression of a repressor and its motif activity.
However, whether the transcription factor is an activator or a repressor, it could regulate the downstream target only when it binds to the cis-regulatory element with its motif. Therefore, even if the transcription factor is a repressor, there should be a positive correlation between its expression and its motif activity, since the transcription factor can only play its role in a cell when its cis-regulatory element is open.
I don't know why some people think there is a negative correlation between the repressor and its motif. Could it be that the motif activity calculated by chromvar is not actually a measure of the accessibility of the genomic region containing the motif, but something else? Can anyone help answer my question?
citing these claims might help get a response...