Modifications (SUMOylation) track

The Modifications (SUMOylation) track predicts sites where lysine undergoes the addition of small, ubiquitin-like modifiers after translation using the approach of Ren et al., 2009. The covalent attachment of this small, ubiquitin-like protein to other proteins can modify and regulate cell function.

Modifications (SUMOylation) provides individual region plots for each of four sumoylation site patterns: KxD, KxE, IKxEP and KxE. The weights for the amino acids in each window are calculated and used for a system of linear equations which result in a correlation coefficient between the training data and the known false pattern positives. This correlation value is used as a threshold for predicting a sumoylation pattern.

To apply this track to the sequence:

In the Tracks panel, check the box next to Modifications (SUMOylation).

The track will now be visible in the Analysis view. The SUMOylation method displays results as "markers" on the synopsis. Expand the groups below the synopsis, if present, to see channels showing different groups and propensities.

To edit method options:

Select the method in the Tracks panel. Open the Track Options section, which appears as follows:

• Threshold (0.0..1.0) – The default value of 0.3 maximizes the correlation coefficient between the training data set and the known false pattern positives. Decreasing this value increases both true positives and false positives; increasing this value decreases false positives at the expense of decreasing true positives as well.

Click if you wish to return to the default settings.