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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.

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

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)  
  1. (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).
  2. (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.