Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data

Table 3 Results of the analysis of the Welsh dataset for down-regulated genes. The different sample clusters found by FADA are shown, together with the significant GO and GenMAPP terms associated to them. The first column shows the cluster number; the second shows the samples associated to that cluster; columns 3 and 4 show the Z-score of the GenMAPP and GO terms associated to the cluster (see Methods); columns 5 to 8 show the corresponding GenMAPP and GO terms selected.

C	SAMPLES	Z(GM)	Z(GO)	GENMAPP	GO(MF)	GO(BP)	GO(CC)
1	LNCaP_A, LNCaP_B, LNCaP_+_DHT	0.36	-0.10 -0.54 4.09				extracellular space (3.74e-04) MHC protein complex (4.71e-04)
2	CAF_1598, BPHF_1598, CAF_1303, CAF_1852, PrSC_A, PrSC_B, CAF_2585, Du145, PC3, HUVEC_A, HUVEC_B, hPr1, PrEC	2.33	2.43 0.68 -0.50	Hs_GPCRDB_Other (1.96e-03) Hs_Ribosomal_Proteins (1.03e-08)	structural constituent of ribosome (2.57e-05) SH3/SH2 adaptor activity (6.48e-03) nucleic acid binding (7.71e-04) oxygen transporter activity (6.93e-03) nucleobase, nucleoside, nucleotide and nucleic acid transporter activity (6.93e-03)
3	B_CELLS_A, B_CELLS_B, B_CELLS_C, MOLT4, HL60	0.91	0.85 -0.65 -0.91
4	T4, T7, T3, T5, T1, T27, T10, T9, T13A, T13B, T22, T12, T29, T8, T31, T30, T26, T19, T16, T23, T6, T24, T21, T11, T17	4.30	1.04 1.86 7.71	G1_to_S_cell_cycle_React (7.76e-04) Glycolysis_and_Gluconeogenesis (4.02e-04) Cell_cycle_KEGG (7.03e-08) DNA_replication_Reactome (2.01e-03)			signalosome complex (5.23e-04) intracellular (4.66e-04) tubulin (2.97e-03) proteasome complex (sensu Eukaryota) (2.47e-04) proton-transporting ATP synthase complex (9.01e-04) Arp2/3 protein complex (5.23e-04)
5	N2, N1, N5, N3, N9, N8, N7, N10, N4	-0.21	-0.65 3.83 -0.53			metabolism (3.90e-04)

(a) GO or GenMAPP terms are discussed in the text. Together with each term, we show the corresponding P-value, according to the hipergeometric distribution (see Methods).
(b) The Z(GO) column shows the Z-scores corresponding to Molecular Function (MF), Biological Process (BP), and Cellular Component (CC), respectively, obtained for each cluster. The Z(GM) column refers to the Z-score corresponding to the GenMAPP terms.

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