[BioC] BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building

Oliver Ruebenacker curoli at gmail.com
Thu May 31 23:47:32 CEST 2012


  I am exploring the idea of creating a package to import pathways as
BioPAX/SBPAX (Level 3) data to analyze various measurements. In
particular, differential microarray measurements could be used to
identify upstream pathway nodes that seem to play a critical role in
explaining the observed differences.

  The basic idea is very simple: consider a pathway that contains
reactions A -> X, B -> X and B -> Y. If measurements show an increase
in X, but not in Y, this would suggest an increase in A. If, however,
we see increases of both X and Y, then this would point to an increase
in B. Analogous considerations apply to nodes upstream of A and B.
Negative correlations (by inhibition or depletion) will also be
included. Consider this applied to a large network and a large set of
measurements, which requires statistical tools to identify the most
relevant upstream nodes.

  There are people using similar methods on similar data relying on
quite simple evaluation functions and turning it into a profitable

  We can start with a simple prototype that can be created and
deployed as quickly as possible as proof of concept to find interested
parties. If there is sufficient interest, a more sophisticated version
can be built.

  Different implementation approaches are possible. It seems to be
simple and efficient to use rjava and have the reaction network
extracted from BioPAX/SBPAX by a Java package that uses OpenRDF Sesame
Rio (i.e. a small fraction of Sesame dealing with RDF graph
representation and I/O).

  Any comment or show of interest is greatly appreciated.


     Take care

Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

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