Pathway topology conversion
BioCarta pathways were retrieved in BioPax format from the PDI
database web page. We define a pathway for each BioPax tag ``pathway''. Pathway nodes
often correspond to multiple gene products. These can be divided into
protein complexes (proteins linked by protein-protein interactions)
and groups made of alternative members (genes with similar biochemical
functions). Thus, when considering signal propagation these groups are
considered differently. The first kind (hereafter group AND) should be
expanded into a clique (all proteins connected to the others), while
the second (hereafter group OR) should be expanded without connection
among them. In the BioPax format only one type of group is allowed:
protein complexes (group AND) with the tag 'complex'. However, it
often happens that the 'protein' tag contains multiple 'xref' pointing
to alternative elements of the process (group OR). Compound mediated interactions are interactions for which a compound
acts as a bridge between two elements. Since chemical compounds are
not usually measured with high-throughput technology, they should be
removed from the network to analyse gene signals. However, the trivial
elimination of the compounds, without signal propagation, will
strongly bias the topology interrupting the signals that pass through
them. If element 'A' is linked to compound 'c' and compound 'c' is
linked to element 'B', element 'A' should be linked to element
'B'. Not all compounds are considered for the propagation because some
of them (for example: H2O, ATP, ADP) are highly frequent in map
descriptions and the signal propagation through them would lead to
chains too long. Compounds not considered for propagation are not
characteristic of a specific reaction, but act as secondary
substrates/products widely shared among different processes. graphite allows the user to see the single/multiple relation types
that characterized an edge. The type of edges have been kept as much
as possible similar to those annotated in the original data
format. Some new types have been introduced due to topological
conversion needs.