Table 3.

Down-regulated pathways in group H or L compared to group M in GSEA enrichment

Hallmark name	Terma description	Set sizeb	NESc	FDR q value
Interferon gamma response§	Genes up-regulated in response to IFNG	200	− 2.82†	0†
			− 2.65‡	0‡
Interferon alpha response§	Genes up-regulated in response to alpha interferon proteins	97	− 2.77†	0†
			− 2.63‡	0‡
Allograft rejection§	Genes up-regulated during transplant rejection	196 †	− 2.52†	0†
		194‡	− 2.42‡	0‡
Oxidative phosphorylation§	Genes encoding proteins involved in oxidative phosphorylation	200	− 1.54†	0.012†
			− 2.40‡	0‡
IL6 JAK STAT3 signaling §	Genes up-regulated by IL6 via STAT3, e.g., during acute phase response	87	− 1.84†	0†
			− 1.56‡	0.016‡
Complement§	Genes encoding components of the complement system, which is part of the innate immune system	198	− 1.82†	0.000†
			− 1.54‡	0.018‡
Inflammatory response§	Genes defining inflammatory response	200	− 2.30†	0†
			− 1.45‡	0.036‡
KRAS signaling up §	Genes up-regulated by KRAS activation	199	− 1.63†	0.004†
			− 1.51‡	0.021‡
TNFA signaling via NFKB†	Genes regulated by NF-kB in response to TNF	200	− 2.09	0
IL2 STAT5 signaling †	Genes up-regulated by STAT5 in response to IL2 stimulation	200	− 1.94	0
Apoptosis†	Genes mediating programmed cell death (apoptosis) by activation of caspases	160	− 1.71	0.001
P53 pathway †	Genes involved in p53 pathways and networks	200	− 1.48	0.022
MYC targets V1‡	A subgroup of genes regulated by MYC version 1 (v1)	200	− 1.64	0.008
DNA repair ‡	Genes involved in DNA repair.	150	− 1.64	0.009
Protein secretion‡	Genes involved in protein secretion pathway.	96	− 1.66	0.009
Adipogenesis‡	Genes up-regulated during adipocyte differentiation (adipogenesis)	198	− 1.61	0.011
Heme metabolism‡	Genes involved in metabolism of heme (a cofactor consisting of iron and porphyrin) and erythroblast differentiation	198	− 1.59	0.012
Fatty acid metabolism‡	Genes encoding proteins involved in metabolism of fatty acids	153	− 1.53	0.017

^aTerm, referred to the MSigDB H (hallmark) term

^bSet size, gene set size after restricting to dataset

^cNES normalized enrichment score. Group M was set as the control group. Negative NES value indicated down-regulation in group H or L

^†referred to comparison L vs. M

^‡referred to comparison H vs. M

^§referred to both comparisons