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Figure 4 | BMC Genomics

Figure 4

From: Reprogramming of lysosomal gene expression by interleukin-4 and Stat6

Figure 4

Correlation of Stat6 with lysosomal genes. Average expression correlations across the indicated number (n) of datasets were calculated between Stat6 and each of (A) 16,771 genes represented on Affymetrix Mouse_430_2 arrays and (F) 17,236 genes represented on HG_U133_Plus2 arrays (see Methods). Only datasets with a coefficient of variation for Stat6 expression of at least 5% were used for analyses. Genes were sorted according to correlation values, and the ranked lists were analyzed using the GSEA tool [57]. Gene set reference files in gene matrix transposed (gmt) format were generated by reformatting lists, downloaded from the AmiGO gene ontology website, containing all mouse and human GO associations (all gene product types and data sources) [38]. Complete results of GSEA and GOstats statistics are given in Additional file 8. (A,F) Average expression correlations with Stat6. (B,G) Running-sum enrichment scores for association with the gene set ‘lysosome’ (GO:0005764; 236 and 230 genes in mouse and human gene sets, respectively); arrows indicate the position of the maximum enrichment score and delimit the ‘leading-edge’ set of genes that account for the enrichment signal associated with the GO term ‘lysosome’ [57]. (C,H) Barcode plots indicate the positions of lysosomal genes along the rank lists. (D,I) Ranks of lysosomal genes that are positively regulated by Stat6 in IL-4 treated mouse macrophages (see Figure 5 and Additional file 9). (E,J) Ranks of lysosomal gene loci bound by Stat6 in mouse macrophages based on data deposited by Ostuni et al. (2013) [58] (see main text). Lines in barcode plots are drawn at 40% transparency.

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