No major promoter when internal promoters are strong

[lukauskas]

Hi again,

While investigating the proActiv results for my sample dataset I came across the fact that many genes do not have a "Major" promoter, yet they tend to have multiple Minor promoters.

This was a bit unexpected as example workflow states the following (emphasis mine):

Promoters are also categorized into three classes. Promoters with activity < 0.25 are classified as inactive, while the most active promoters of each gene are classified as major promoters. Promoters active at lower levels are classified as minor promoters.

I now realise that this is related to the other statement described in limitations section:

proActiv will not provide promoter activity estimates for promoters which are not uniquely identifiable from splice junctions (single exon transcripts, promoters which overlap with internal exons).

Which makes sense. Looking at the source code, I believe this limitation is implemented as internalPromoter column in the output of proActiv.

In the actual implementation, specifically these lines, the "Major/Minor" classification is assigned before filtering out the internal promoters though.

In cases where an internalPromoter has higher activity than any non internal promoter, this would result this internal promoter being assigned the Major tag in the code. This assignment would be overwritten with NA immediately, but no other promoter being selected as Major leaving only Minor promoters and NAs.

• Is this expected?
• Shouldn't one of the otherwise Minor promoters that are not internalPromoter be assigned the Major label in these cases?

[jonathangoeke]

Hi @lukauskas this is a very good question, and I think this will be relevant to other users as well. proActiv is now hosted on Bioconductor (you can install the latest version here: https://www.bioconductor.org/packages/release/bioc/html/proActiv.html). Would you mind posting this question to the Bioconductor forum? https://support.bioconductor.org/ We will respond there so others can easily find this.

[lukauskas]

Sure: https://support.bioconductor.org/p/p132561/