Table 2.

Dysregulated biological pathways in tumor tissues

Direction	KEGG pathway	Size	ESa	NESb	p value	FDRc
Upregulated	Cell cycle	73	0.50	2.10	< 0.001	6.54E−04
	Pyrimidine metabolism	34	0.55	2.01	< 0.001	8.94E−04
	Spliceosome	39	0.52	2.01	< 0.001	1.01E−03
	Base excision repair	16	0.65	2.01	< 0.001	1.07E−03
	Proteasome	35	0.55	2.04	< 0.001	1.12E−03
	Aminoacyl TRNA biosynthesis	18	0.62	1.95	< 0.001	1.34E−03
	Ubiquitin-mediated proteolysis	87	0.47	2.06	< 0.001	1.35E−03
	DNA replication	17	0.61	1.92	< 0.001	1.93E−03
	RNA degradation	22	0.54	1.84	2.41E−03	4.65E−03
	Homologous recombination	15	0.59	1.76	6.51E−03	1.32E−02
	Nucleotide excision repair	22	0.50	1.69	9.64E−03	2.51E−02
	N glycan biosynthesis	19	0.51	1.69	7.17E−03	2.66E−02
Downregulated	Hematopoietic cell lineage	47	− 0.51	− 2.77	< 0.001	< 0.0001
	Graft versus host disease	24	− 0.61	− 2.72	< 0.001	< 0.0001
	Complement and coagulation cascades	36	− 0.50	− 2.54	< 0.001	< 0.0001
	Allograft rejection	23	− 0.40	− 2.29	< 0.001	6.10E−04
	Asthma	20	− 0.35	− 2.37	< 0.001	7.12E−04
	Neuroactive ligand receptor interaction	88	− 0.56	− 2.44	< 0.001	8.55E−04
	Vascular smooth muscle contraction	61	− 0.55	− 2.47	< 0.001	1.07E−03
	Autoimmune thyroid disease	23	− 0.46	− 2.11	< 0.001	4.96E−03
	Cell adhesion molecules cams	78	− 0.33	− 2.03	< 0.001	7.04E−03
	Calcium signaling pathway	76	− 0.31	− 2.01	< 0.001	7.55E−03
	Dilated cardiomyopathy	43	− 0.35	− 1.90	9.26E−03	9.91E−03
	Viral myocarditis	46	− 0.32	− 1.79	9.90E−03	2.28E−02
	Leukocyte transendothelial migration	65	− 0.29	− 1.77	< 0.001	2.50E−02
	PPAR signaling pathway	21	− 0.34	− 1.67	2.90E−02	3.85E−02
	Intestinal immune network for IGA production	31	− 0.39	− 1.69	2.45E−02	3.86E−02
	Cytokine cytokine receptor interaction	142	− 0.29	− 1.64	1.85E−02	4.21E−02
	Leishmania infection	53	− 0.24	− 1.65	< 0.001	4.36E−02

^aEnrichment score for the gene set;

^bnormalized enrichment score, the enrichment score for the gene set after it has been normalized across analyzed gene sets;

^cfalse discovery rate of NES