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. Author manuscript; available in PMC: 2019 May 3.
Published in final edited form as: Mol Cell. 2018 May 3;70(3):531–544.e9. doi: 10.1016/j.molcel.2018.03.037

Figure 4. Loss of PI5P4Ks induces autophagy-lysosome gene program and metabolic deficiencies.

Figure 4

(A) Pathway enrichment for genes significantly differentially expressed (47 Genes, False Discovery Rate (FDR) <0.2) and overlapping Autophagy Signature (Perera et al., 2015), between control and double knockout MEFs. Ranked by −log10 (p-value).

(B) Normalized enrichment score (NES) for genes identified as part of the KEGG Lysosomal and Hallmark mTORC1 gene sets. The upper part shows the NES, which is calculated by ranked ordered gene set, increasing the score when a gene is in the set and decreasing it when it is not. Each blue line represents a hit from the gene set. The lower portion shows the rank ordered genes for the double knockout MEFs when compared to the control MEFs, with highly expressed to the far left and down-regulated genes to the right. Enrichment score (ES) for KEGG Lysosome=0.62 and Hallmark mTORC1 = −0.49, FDR < 0.2 for both.

(C) Heat map of lysosomal genes and mTORC1 genes from (B). P-values were adjusted for multiple testing using the Benjamini-Hochburg method with p < 0.05 and q < 0.1, (n = 3).