Transcriptional Profiling of Pten Knockout Mice

Gene expression profiling (GEP) was done using the MouseRef-8 v2.0 Expression BeadChip (Illumina, San Diego, CA, USA), following the manufacturer’s protocol. Arrays were read on an Illumina HiScanSQ system. Data were first extracted with the Illumina GenomeStudio software and then imported in Genomics Suite 6.4 (Partek Incorporated, Saint Louis, MO USA) and quantile normalized. Transcripts with differences in expression were identified by ANOVA. Enrichment analysis was performed using Gene Set Enrichment Analysis (GSEA) 56 (link). Raw data have been deposited in National Center for Biotechnology Information’s Gene Expression Omnibus (GEO) and are accessible through GEO accession no. GSE74245. GSEA was performed on entire gene list ranked according to fold changes observed between Pten^pc-/- and Pten^pc-/-; Pdha1^pc-/Y mice. The GS collection assessed includes all GSs smaller than 10 and larger than 500 (8335 out of 22423 GSs retained) compiled according to57 (link) the 24.03.15. GSs yielding significance ((FDR <0.05; nominal p-value <0.005; TAGS ≥50%) were retained and assessed for their role in metabolic processes after visualizing the data as described 58 (link). For the 3 relevant clusters identified, their GSs’ FDR q-values were, together with unaffected metabolic processes log2 transformed and inversed for display in Fig. 2a.