Fig. 3

Pathway and gene set enrichment analysis. a Workflow of pathway and gene set enrichment analysis between ALDH7A1 high and low expression groups of LIHC and KIRC patients. Low expressed genes were filtered out by requiring RSEM > 10 in > 33% of patients. Genes differentially expressed between the low and high ALDH7A1 mRNA tumor groups were selected using a minimum threshold of +/− 0.4 log₂-fold change, with an adjusted p-value of < 0.05. Fold change and p-values were used according to requirements of each specific method. Six different R packages (ESEA, GRAPHITE, SPIA, CEPA, PIANO and GAGE) were applied to the Reactome, BioCarta, NCI and KEGG pathway databases and the MsigDB gene set annotation collections, as indicated. b Summary of significantly affected pathways and biological processes after filtering. ↓ - pathway inactivated /down regulated; ↑ pathway activated /up regulated, ↕ - direction not provided. Light blue – amino acid metabolism; bright red – PPAR signaling pathway; light violet – energy metabolism; dark red – bile acid metabolism; light green – lipid, fatty acid metabolism; light orange - processes related to cell motility. c Map of the PPAR signaling pathway from the KEGG database, showing genes that were differentially expressed in LIHC tumors with low ALDH7A1 expression. Scale – log₂FC; Blue: lower expression in tumors. Red: higher expression in tumors. Image rendered by Pathview [28]