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

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

2012-01-10

arxiv.org/abs/1201.2033v2

Biology

Quantitative Biology

Molecular Networks

8 pages, 4 figures, 4tables. Formated version. Submitted to Bioinformatics

Scientific paper

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: mbellis@crbm.cnrs.fr. Supplementary information: Supplementary data are available at http://bns.crbm.cnrs.fr/download.html.

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