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. Author manuscript; available in PMC: 2012 May 27.
Published in final edited form as: Cancer Cell. 2012 Jan 17;21(1):105–120. doi: 10.1016/j.ccr.2011.12.006

Figure 4. Gene Ontology and Gene Set Enrichment Analyses between Pancreata from Pdx1-Cre;KrasLSL-G12D and Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F Mice and Profiling Cytokine Expression.

Figure 4

(A) Enriched expression of NF-κB downstream target gene sets in Pdx1-Cre;KrasLSL-G12D;IKK2/βWT compared to Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F. The heat map represents top enriched genes in Pdx1-Cre;KrasLSL-G12D;IKK2/βWT. NES, normalized enrichment score; NOM p value, nominal p value; FDR, false discovery rate q value. (red, high expression; blue, low expression).

(B) GSEA analyses identify the enriched gene sets expressed either in Pdx1-Cre;KrasLSL-G12D;IKK2/βWT or Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F using 198 KEGG pathway gene sets. One gene set are enrich in Pdx1-Cre;KrasLSL-G12D;IKK2/βWT and twenty seven gene sets are enriched in Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F. Five NF-κB pathway-related gene sets are noteworthy enriched in Pdx1-Cre;KrasLSL-G12D; IKK2/βWT. Enriched gene sets were selected based on statistical significance (FDR q value < 0.25 and normalized p value < 0.05).

(C) GSEA analyses of significant gene upregulation in Pdx1-Cre;KrasLSL-G12D revealed that they are strongly correlated to positive nodal status, high risk, higher tumor stage, and poor survival in PDAC patients by using 102 PDAC cDNA microarray data (GSE21501). Two- and 5-fold enriched expression in Pdx1-Cre;KrasLSL-G12D; IKK2/βF/F is correlated to low risk. ns, not significant (FDR q value > 0.25 and/or normalized p value > 0.05).

(D) Analysis of differential cytokine gene expression between pancreatic cancer and normal pancreas (from 5- to 12-month-old Pdx1-Cre;KrasLSL-G12D mice and age-matched Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F mice) by real-time PCR arrays.

(E) Determination of IL-1α expression levels in pancreas, liver, and lung from Pdx1-Cre;KrasLSL-G12D, Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F, Pdx1-Cre;IKK2/βF/F, and wild-type (WT) mice.

(F) Evaluation of IL-1α and IL-1β expression levels in sera from Pdx1-Cre;KrasLSL-G12D, Pdx1-Cre;KrasLSL-G12D;IKK2/βF/F, Pdx1-Cre;IKK2/βF/F, and wild-type (WT) mice. Error bars represent ±SD of the data from three mice in each genotype as indicated. See also Figure S2 and Tables S1–S3.