Skip to main content

Table 2 Results of the analysis of the Welsh dataset for up-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 7.22 5.09
-0.39
2.59
RNA_transcription_React. (2.40e-03)
Electron_Transport_Chain (5.74e-10)
oxidoreductase activity (1.58e-04)
carrier activity (1.87e-04)
ATPase activity, coupled to transmembrane movement of substances (4.23e-03)
transcriptional activator activity (2.09e-03)
  intracellular organelle (5.48e-04)
2 CAF_1598, BPHF_1598
CAF_1303, CAF_1852
PrSC_A, PrSC_B, CAF_2585, Du145, PC3, HUVEC_A, HUVEC_B, hPr1, PrEC
3.83 4.66
2.74
5.13
Hypertrophy_model (8.97e-03)
Proteasome_Degradation (1.44e-08)
Cell_cycle_KEGG (7.86e-03)
Pentose_Phosphate_Pathway (4.89e-03)
Enzyme inhibitor activity (4.96e-04)
hydrolase activity (9.26e-03)
small protein conjugating enzyme activity (3.54e-04)
structural constituent of cytoskeleton (2.73e-03)
nucleotide binding (1.17e-05)
regulation of cellular process (4.31e-03)
cellular physiological process (1.93e-04)
signalosome complex (7.27e-03)
membrane coat adaptor complex (4.24e-03)
tubulin (5.06e-06)
proteasome complex (sensu Eukaryota)(3.69e-07)
Arp2/3 protein complex (4.19e-05)
3 B_CELLS_A, B_CELLS_B B_CELLS_C, MOLT4, HL60 4.27 0.42
0.18
-0.04
mRNA_processing_React. (2.10e-03)
G1_to_S_cell_cycle_React. (9.25e-05)
Cell_cycle_KEGG (1.94e-04)
Small_ligand_GPCRs (5.52e-03)
Ovarian_Infertility_Genes (5.19e-03)
GPCRDB_Class_C_Metabotropic_glutamate_pheromone (4.72e-04)
   
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 2.06 1.93
0.39
0.76
Fatty_Acid_Degradation (8.48e-03)
Hypertrophy_model (3.34e-03)
Eicosanoid_Synthesis (3.56e-03)
steroid binding (7.57e-03)
isomerase activity (7.99e-04)
vitamin binding (6.99e-04)
  
5 N2, N1, N5, N3, N9, N8, N7, N10, N4 6.86 2.52
-0.31
-0.40
Smooth_muscle_contraction (6.55e-03)
Calcium_reg_in_card_cells (3.97e-03)
channel or pore class transporter activity (1.75e-03)
structural constituent of cytoskeleton (2.75e-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 Celular Component (CC), respectively, obtained for each cluster. The Z(GM) column refers to the Z-score corresponding to the GenMAPP terms.