常用Hallmark及KEGG、GO基因查询

文献：The Molecular Signatures Database (MSigDB) hallmark gene set collection - PMC (nih.gov)

 GSEA | MSigDB | Browse Human Gene Sets (gsea-msigdb.org)通过msigdb数据库可以查看各个Hallmark、KEGG、GO具体包含的基因细节。

Hallmark name	Process category	Description	Number of founder sets	Number of genes
1	APICAL_JUNCTION	cellular component	Apical junction complex consisting of adherens and tight junctions	37	200
2	APICAL_SURFACE	cellular component	Membrane proteins in the apical domain	12	44
3	PEROXISOME	cellular component	Peroxisomes	28	107
4	ADIPOGENESIS	development	Adipocyte development	36	200
5	ANGIOGENESIS	development	Blood vessel formation	14	36
6	EPITHELIAL_MESENCHYMAL_TRANSITION	development	Epithelial mesenchymal transition	107	200
7	MYOGENESIS	development	Muscle differentiation	64	200
8	SPERMATOGENESIS	development	Sperm development and male fertility	24	135
9	PANCREAS_BETA_CELL	development	Genes specific to pancreatic beta cells	24	40
10	DNA_REPAIR	DNA damage	DNA repair	44	150
11	UV_RESPONSE_DOWN	DNA damage	UV response: down-regulated genes	17	144
12	UV_RESPONSE_UP	DNA damage	UV response: up-regulated genes	16	158
13	ALLOGRAFT_REJECTION	immune	Allograft rejection	190	200
14	COAGULATION	immune	Coagulation cascade	71	138
15	COMPLEMENT	immune	Complement cascade	71	200
16	INTERFERON_ALPHA_RESPONSE	immune	Interferon alpha response	82	97
17	INTERFERON_GAMMA_RESPONSE	immune	Interferon gamma response	82	200
18	IL6_JAK_STAT3_SIGNALING	immune	IL6 STAT3 signaling during acute phase response	24	87
19	INFLAMMATORY_RESPONSE	immune	Inflammation	120	200
20	BILE_ACID_METABOLISM	metabolic	Biosynthesis of bile acids	28	112
21	CHOLESTEROL_HOMEOSTASIS	metabolic	Cholesterol homeostasis	28	74
22	FATTY_ACID_METABOLISM	metabolic	Fatty acid metabolism	53	158
23	GLYCOLYSIS	metabolic	Glycolysis and gluconeogenesis	87	200
24	HEME_METABOLISM	metabolic	Heme metabolism	36	200
25	OXIDATIVE_PHOSPHORYLATION	metabolic	Oxidative phosphorylation and citric acid cycle	93	200
26	XENOBIOTIC_METABOLISM	metabolic	Metabolism of xenobiotics	124	200
27	APOPTOSIS	pathway	Programmed cell death; caspase pathway	80	161
28	HYPOXIA	pathway	Response to hypoxia; HIF1A targets	87	200
29	PROTEIN_SECRETION	pathway	Protein secretion	74	96
30	UNFOLDED_PROTEIN_RESPONSE	pathway	Unfolded protein response; ER stress	22	113
31	REACTIVE_OXYGEN_SPECIES_PATHWAY	pathway	Reactive oxygen species (ROS) pathway	13	49
32	E2F_TARGETS	proliferation	E2F targets	420	200
33	G2M_CHECKPOINT	proliferation	Cell cycle G2/M checkpoint	420	200
34	MYC_TARGETS_V1	proliferation	MYC targets variant 1	404	200
35	MYC_TARGETS_V2	proliferation	MYC targets variant 2	6	58
36	P53_PATHWAY	proliferation	p53 pathway	85	200
37	MITOTIC_SPINDLE	proliferation	Mitotic spindle assembly	108	200
38	ANDROGEN_RESPONSE	signaling	Androgen response	8	117
39	ESTROGEN_RESPONSE_EARLY	signaling	Early estrogen response	61	200
40	ESTROGEN_RESPONSE_LATE	signaling	Late estrogen response	61	200
41	IL2_JAK_STAT5_SIGNALING	signaling	IL2 STAT5 signaling	13	200
42	KRAS_SIGNALING_UP	signaling	KRAS signaling, up-regulated genes	14	200
43	KRAS_SIGNALING_DOWN	signaling	KRAS signaling, down-regulated genes	16	200
44	MTORC1_SIGNALING	signaling	mTORC1 signaling	487	200
45	NOTCH_SIGNALING	signaling	Notch signaling	49	32
46	PI3K_AKT_MTOR_SIGNALING	signaling	PI3K signaling via AKT to mTORC1	591	105
47	HEDGEHOG_SIGNALING	signaling	Hedgehog signaling	79	36
48	TGF_BETA_SIGNALING	signaling	TGF beta signaling	29	54
49	TNFA_SIGNALING_VIA_NFKB	signaling	TNFA signaling via NFkB	132	200
50	WNT_BETA_CATENIN_SIGNALING	signaling	Cannonical beta catenin pathway	49	42

例如查询EMT基因集：

REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION (gsea-msigdb.org)

（需要先使用edu邮箱进行注册）

ARHGEF18
CGN
F11R
FKBP1A
PARD3
PARD6A
PRKCZ
RHOA
RPS27A
SMURF1
TGFB1
TGFBR1
TGFBR2
UBA52
UBB
UBC
参考文献：

1：The Molecular Signatures Database (MSigDB) hallmark gene set collection