Extended Data Fig. 4: PSME4 low tumors are enriched in T cell pathways with proteomics but not transcriptomics.
a – c, Pathway enrichment analysis was performed for the tumors in the CPTAC-LUAD cohort that are defined as PSME4 enriched (based on Fig. 1) using the (a) KEGG (b) BIOCARTA or (c) Gene Ontology datasets. The Normalized Enrichment score (for the PSME4-low tumors compared to the PSME4-high tumors) is plotted with the circle size indicated pathway size and the color indicating the significance of the enrichment determined by FDR corrected q-value (n = 111 tumors). d, qPCR of PSME4 in A549 cell line following depletion of PSME4 with shA223 or shA073 compared to shCtrl with and without stimulation with TNFα and IFNγ (T + I) (two-sided paired student’s T test, P values in source data.; n = 3 independent biological experiments; bars indicate mean ± s.d.). e, Lysates of A549 cells with PSME4 knockdown (shA223 and shA073) or control (shCtrl) were blotted for PSME4 and β-Actin as a loading control. The experiment was repeated twice with similar results. f, Quantification of PSME4 band intensity in A549 cell line with PSME4 KD (A223 or A073) or shCtrl (Ctrl) across three independent samples normalized to actin as a loading control and to shCtrl (Welch’s corrected two-sided student’s T-test *P = 0.0186; ***P = 0.0005; bars indicate mean ± s.d.). g, The fold change in gene expression between the A549 cell line following depletion of PSME4 with shA223 compared to shCtrl is plotted against the significance of the change. Genes which passed the FDR adjusted P value cutoff of 0.05 are presented. Significance is determined by Wald test with BH correction.
