CIM Schroedinger Eigenmaps III We have labeled transcription factors (CHX10, OTX2, PAX6) that are known from the literature to be associated to development. We intend to derive a cluster whose GO categories are specific to eye development when starting with labeled genes. Schroedinger Eigenmaps using these labels is applied and the new data representation is then clustered. The three labeled TF are contained in the same cluster with 154 other genes. GoMiner enrichment analysis leads to relatively generic categories that one would expect from the choice of the labeled TF. However, specific eye development categories were not found. This observation suggests that gene labeling based on literature search leads to relatively poor GoMiner enrichments.
Ehler et al. BMC Proceedings 2011 5(Suppl 2):S3 doi:10.1186/1753-6561-5-S2-S3