Affinity summarisation

To get TF scores for a gene, STARE summarises the TF-affinities from regions that were assigned to that gene. Since STARE offers different approaches to get the region-gene mapping, it also has different ways to summarise the TF affinities.

The basic idea is always the same. We sum up the tf affinities of the regions r that were linked to a gene g:

STARE_BaseEquation

Now the scaler is where it changes depending on how the region-gene mapping was done. The different approaches make use of different types of data, which allows to integrate more data modalities. When running in promoter-mode without any bed-file, we don’t have any information for scaling, and thus, the scaler is 1.

Gene window

In case that all regions within a window around the TSS are considered relevant, the equation would change to the following:

STARE_WindowEquation

The scaling with the activity of the region is only done when activity columns were specific (-n). The scaling with the exponential decay function can be turned off with -e False, for example for very small window sizes. The distance decay can only be turned off for the Gene window-version, for the ABC-mode it is always on.

ABC-scoring

If you did the region-gene mapping with the ABC-score, we change the scaling and also distinguish between regions close to the promoter and more distant ones. The reason is that the measurement of contact frequency of a region with itself is likely flawed. Note that the -e flag for the distance decay does not change the scaling here.

STARE_AdaptedABCEquation

Not-adapted ABC-scoring

If you chose to run the ABC-scoring without the adapted score, we can’t use the adapted activity for scaling. Thus, the affinity scaling changes to:

STARE_UnadaptedABCEquation

The -e flag also doesn’t change the scaling in this setup.