Mapping of Affymetrix probe sets to groups of transcripts using transcriptional networks

Motivation: Usefulness of analysis derived from Affymetrix microarrays depends largely upon the reliability of files describing the correspondence between probe sets, genes and transcripts. In particular, in case a gene is targeted by two probe sets, one must be able to assess if the corresponding signals measure a group of common transcripts or two groups of transcripts with little or no overlap. Results: Probe sets that effectively target the same group of transcripts have specific properties in the trancriptional networks we constructed. We found indeed that such probe sets had a very low negative correlation, a high positive correlation and a similar neighbourhood. Taking advantage of these properties, we devised a test allowing to group probe sets which target the same group of transcripts in a particular network. By considering several networks, additional information concerning the frequency of these associations was obtained. Availability and Implementation: The programs developed in Python (PSAWNpy) and in Matlab (PSAWNml) are freely available, and can be downloaded at http://code.google.com/p/arraymatic/. Tutorials and reference manuals are available at http://bns.crbm.cnrs.fr/softwares.html. Contact: [email protected]. Supplementary information: Supplementary data are available at http://bns.crbm.cnrs.fr/download.html.