Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

BMC Cancer

Table 3 Pathways identified by GennMAPP analysis

Pathway	Ams	Hua	HUM	Rot	S03	S06	Sto	Upp	mean	p	FDR
Up-regulated
Hs_Cell_cycle_KEGG	1	97	2	1	1	4	1	1	13.5	< 10E-6	9.0E-5
Hs_Cell_Cycle-G1_to_S_control_Reactome	3	51	21	13	5	7	8	11	14.9	< 10E-6	9.0E-5
Hs_DNA_replication_Reactome	2	124	3	8	6	10	2	3	19.8	5.0E-6	3.0E-4
Hs_Electron_Transport_Chain	73	9	34	2	35	11	4	2	21.3	1.0E-5	4.4E-4
Hs_Androgen-Receptor_NetPath_2	82	12	9	16	20	5	43	19	25.8	4.6E-5	1.3E-3
Hs_1-Tissue-Embryonic_Stem_Cell	6	157	1	4	22	3	13	4	26.3	5.2E-5	1.3E-3
Hs_mRNA_processing_Reactome	45	22	64	6	33	26	9	5	26.3	5.2E-5	1.3E-3
Hs_Citrate_cycle_TCA_cycle_	18	23	81	40	7	35	11	21	29.5	1.5E-4	3.3E-3
Hs_Aminoacyl_tRNA_biosynthesis	19	101	84	32	10	13	3	8	33.8	4.7E-4	9.3E-3
Hs_Cholesterol_Biosynthesis	28	119	7	41	13	56	6	24	36.8	1.0E-3	1.8E-2
Hs_Hedgehog_Netpath_10	41	5	4	21	99	18	76	65	41.1	2.7E-3	4.3E-2
Down-regulated
Hs_Adipogenesis	4	22	41	43	16	58	2	1	23.4	2.5E-5	4.4E-3
Hs_EGFR1_NetPath_4	5	3	42	44	24	13	13	80	28.0	1.0E-4	8.9E-3
Hs_T-Cell-Receptor_NetPath_11	37	2	75	6	38	28	19	51	32.0	3.0E-4	1.8E-2
Hs_Smooth_muscle_contraction	30	51	36	23	34	50	12	44	35.0	6.6E-4	2.4E-2
Hs_Insulin_Signaling	15	11	54	64	39	47	16	39	35.6	7.7E-4	2.4E-2
Hs_IL-6_NetPath_18	16	8	163	3	41	7	26	23	35.9	8.1E-4	2.4E-2
Hs_IL-7_NetPath_19	7	5	141	9	19	15	28	78	37.75	1.3E-3	3.0E-2
Hs_IL-3_NetPath_15	58	7	56	18	32	29	44	61	38.125	1.4E-3	3.0E-2

The ranking numbers indicate the ranking of each gene set (pathway) out of the 177 gene sets in each data set and the mean ranking number indicate the ranking in the meta-analysis. Only 19 significant out of a total of 177 gene sets are shown. Ams: Amsterdam, Hua: Huang, HUM: HUMAC, Rot: Rotterdam, S03: Sotiriou 2003, S06: Sotiriou 2006, Sto: Stockholm, Upp: Uppsala.

ISSN: 1471-2407