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.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us