Methods

This Java project which is a module of PathwayMatcher. It defines the procedures to do proteoform matching, search for pathways and do pathway analysis.

Proteoform matching

There are a set of rules to decide if a proteoform in the input sample for PathwayMatcher can be considered the same proteoform in the reference data (Reactome).

PathwayMatcher allows the user to select multiple modes depending on the needs:

• superset: the input proteoform PTMs are superset of the PTMs in the reference proteoform
• subset: the input proteoform PTMs are subset of the PTMs in the reference proteoform
• one: the reference proteoform has at least one input PTM; or the reference has no PTMs
• superset_no_types: similar to superset ignoring the modification types
• subset_no_types: : similar to subset ignoring the modification types
• one_no_types: similar to one ignoring the modification types
• strict: the input and reference proteoforms must match exactly in all the attributes.

The classes implementing that functionality are located here. For mode details on each of this modes please consult this wiki page.

Pathway search

The procedure to find the set of pathways, with their respective reactions, that contain as participants at least one of the entities(genes, proteins, proteoforms...) in the input sample.

Pathway analysis

The java classes that define methods to decide which pathways are more statistically significant to the sample. The implemented method is Over Representation Analysis^[1], assuming that the input list of entities (genes, proteins,...) are differentially expressed and were selected using a cut off threshold.

This set of classes can be extended to include other methods for pathway analysis by following a similar structure with the same input and output data structures.

References

[1] García-Campos, M. A., Espinal-Enríquez, J. & Hernández-Lemus, E. Pathway Analysis: State of the Art. Frontiers in Physiology 6, doi:10.3389/fphys.2015.00383 (2015).