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Table 1 Pathway enrichment analysis with ReactomePA. Only the results relevant to the comparison of O-glycosylation, immune response and complement pathways are reported. For the full list of results, one could refer to our Github repository for the project. We reported only the pathways and genes identified by the initial consensus DEA and the DE genes from the DEA comparisons accounting for the tumor  microenvironment. The range of FDR values identified for that pathway from the different enrichment analyses are reported as a reference

From: Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response

Pathway ID Description FDR Gene IDs
913709 O-linked glycosylation of mucins 0.007–0.04 LUAD (up): B3GNT6/MUC16/MUC21/MUC5B
913709 O-linked glycosylation of mucins 0.01–0.07 LUSC (down): B3GNT7/B3GNT8/GALNT10/GALNT5/MUC1/MUC15/MUC21/MUC5B/ST6GALNAC4
977068 Termination of O-glycan biosynthesis 0.01–0.07 LUAD (up):MUC16/MUC21/MUC5B
5173105 O-linked glycosylation 0.01–0.05 LUAD (up): B3GNT6/ MUC16/MUC21/ MUC5B
5173105 O-linked glycosylation 0.01–0.03 LUSC (down): B3GNT7/B3GNT8/GALNT10/GALNT5/MUC1/MUC15/
977606 Regulation of Complement cascade 0.0002–0.06 LUSC (down):C3/C5/CD55/CFI
166658 Complement cascade 0.0008–0.06 LUSC (down): C3/C5/CD55/CFI