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Table 1 Results of the analysis of the yeast dataset [13]. The different clusters found by FADA are shown, together with the significant GO terms associated to them. The samples belonging to each one of the clusters are also shown. The first column shows the cluster number; the second shows the conditions associated to that cluster; columns 3 to 5 show the Z-score of the GO terms associated to the cluster (see Methods) at the Cellular Component (CC), Biological Process (BP) and Molecular Function (MF) levels; columns 6 to 8 show the corresponding GO terms.

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 CONDITIONS Z(CC) Z(BP) Z(MF) GO(CC) GO(BP) GO(MF)
1 Heat_Shock_05_minutes_hs.1, Heat_Shock_10_minutes_hs.1
Heat_Shock_15_minutes_hs.1, Heat_Shock_20_minutes_hs.1
Heat_Shock_30_minutes_hs.1, Heat_Shock_40_minutes_hs.1
Heat_Shock_60_minutes_hs.1, Heat_Shock_80_minutes_hs.1
Heat_Shock_015_minutes_hs.2, Heat_Shock_030minutes_hs.2
heat_shock_17_to_37._20_minutes, heat_shock_21_to_37._20_minutes heat_shock_25_to_37._20_minutes, heat_shock_29_to_37._20_minutes heat_shock_33_to_37._20_minutes 29C_to_33C_._5_minutes, 29C_to_33C_._15_minutes
29C_.1M_sorbitol_to_33C_._1M_sorbitol_._5_minutes
29C_.1M_sorbitol_to_33C_._1M_sorbitol_._15_minutes
29C_.1M_sorbitol_to_33C_._.NO_sorbitol_._5_minutes
dtt_240_min_dtt.2 1M_sorbitol_._5_min
1M_sorbitol_._15_min 1M_sorbitol_._30_min
1M_sorbitol_._45_min_ DBY7286_37degree_heat_._20_min
DBYmsn2.4._37degree_heat_._20_min
DBYmsn2.4_.real_strain._._37degrees_.20_min.
DBYyap1._37degree_heat_._20_min_.redo.
DBYyap1_._37degree_heat_.repeat., DBYyap1_._0.32_mM_H2O2_.20_min. Msn2_overexpression_.repeat.
Msn4_overexpression
3.25 5.39 1.16 nucleolus (325/88;0.81E-006) ribosome biog. & ass. (271/75; 0.57E-007) response to stress (214/52; 0.26E-003)  
2 constant_0.32_mM_H2O2_.10_min._redo
constant_0.32_mM_H2O2_.20_min._redo
constant_0.32_mM_H2O2_.30_min._redo
constant_0.32_mM_H2O2_.40_min._rescan
constant_0.32_mM_H2O2_.50_min._redo
constant_0.32_mM_H2O2_.60_min._redo
1.5_mM_diamide_.5_min. 1.5_mM_diamide_.10_min.
1.5_mM_diamide_.20_min. 1.5_mM_diamide_.30_min.
1.5_mM_diamide_.40_min. 1.5_mM_diamide_.50_min.
1.5_mM_diamide_.60_min. 1.5_mM_diamide_.90_min.
DBY7286_._0.3_mM_H2O2_.20_min.
DBYmsn2msn4_.good_strain._._0.32_mM_H2O2
DBYmsn2.4_.real_strain._._0.32_mM_H2O2_.20_min.
DBYyap1._._0.3_mM_H2O2_.20_min.
0.39 9.71 11.40   protein catabolism (114/28; 0.74E-017) cell homeostasis (54/8; 0.10E-003) peptidase activity (125/25; 0.17E-012) oxidored. Act. (263/30; 0.36E-008)
3 2.5 mM_DTT_045_min_dtt.1 2.5 mM_DTT_060_min_dtt.1
2.5 mM_DTT_090_min_dtt.1 2.5 mM_DTT_120_min_dtt.1
2.5 mM_DTT_180_min_dtt.1 dtt_120_min_dtt.2
6.55 2.53 1.86 endoplasmic ret. (353/27; 0.11E-008)   
4 constant_0.32_mM_H2O2_.80_min._redo
constant_0.32_mM_H2O2_.100_min._redo
constant_0.32_mM_H2O2_.120_min._redo
constant_0.32_mM_H2O2_.160_min._redo
1.25 0.63 1.58    
5 37_deg_growth_ct.1 NA NA NA    
6 Nitrogen_Depletion_8_h Nitrogen_Depletion_12_h
Nitrogen_Depletion_1_d Nitrogen_Depletion_2_d
Nitrogen_Depletion_3_d Nitrogen_Depletion_5_d
7.11 5.30 0.61 plasma membrane (197/16; 0.86E-005)
extracellular region (19/4; 0.85E-004)
transcription (225/15 0.57E-003)  
7 diauxic_shift_timecourse_18.5_h
diauxic_shift_timecourse_20.5_h YPD_6_h_ypd.2
YPD_8_h_ypd.2 YPD_10_h_ypd.2 YPD_12_h_ypd.2
YPD_1_d_ypd.2 YPD_2_d_ypd.2 YPD_3_d_ypd.2
YPD_5_d_ypd.2 YPD_stationary_phase_12_h_ypd.1
YPD_stationary_phase_1_d_ypd.1
YPD_stationary_phase_2_d_ypd.1
YPD_stationary_phase_3_d_ypd.1
YPD_stationary_phase_5_d_ypd.1
YPD_stationary_phase_7_d_ypd.1
YPD_stationary_phase_13_d_ypd.1
YPD_stationary_phase_22_d_ypd.1
YPD_stationary_phase_28_d_ypd.1
ethanol_vs._reference_pool_car.1
YP_ethanol_vs_reference_pool_car.2
9.91 #### 5.51 ribosome (368/126; 0.20E-010)
peroxisome (52/22; 0.66E-004)
protein biosynthesis (493/168; 0.12E-012)
vitamin metabolism (48/20; 0.27E-003)
structural mol act (359 /119; 0.13E-006)
8 aa_starv_0.5_h aa_starv_1_h aa_starv_2_h aa_starv_4_h
aa_starv_6_h Nitrogen_Depletion_30_min.
Nitrogen_Depletion_1_h Nitrogen_Depletion_2_h
Nitrogen_Depletion_4_h
3.60 #### 4.66 peroxisome (52/6; 0.14E-003)
plasma membrane (197/17; 0.35E-006)
aminoacid metab (173/42; 0.24E-031) transporter act (343/27; 0.12E-004)
lyase activity (97/12; 0.24E-004)
9 33C_vs._30C_._90_minutes dtt_480_min_dtt.2
steady_state_36_dec_C_ct.2
steady_state_36_dec_C_ct.2_.repeat_hyb._
0.12 -1.42 -0.24    
10 dtt_060_min_dtt.2 YP_galactose_vs_reference_pool_car.2
YP_raffinose_vs_reference_pool_car.2
1.43 0.12 -1.53    
11 Diauxic_Shift_Timecourse_._0_h
diauxic_shift_timecourse_9.5_h diauxic_shift_timecourse11.5_
2.86 1.16 0.44 vacuole (140/6; 0.63E-003)   
12 YPD_stationary_phase_2_h_ypd.1
YPD_stationary_phase_4_h_ypd.1
-0.39 3.11 2.06   electron transport (14/1; 0.91E-003)  
13 diauxic_shift_timecourse_13.5_h
diauxic_shift_timecourse_15.5_h
YPD_stationary_phase_8_h_ypd.1
-0.51 -0.27 -0.20    
14 1M_sorbitol_._60_min 1M_sorbitol_._90_min
1M_sorbitol_._120_min
1.21 2.46 1.33   cell cycle (115/4; 0.11E-003)  
15 YPD_2_h_ypd.2 YPD_4_h_ypd.2 YAP1_overexpression -0.34 0.20 0.56    
16 1_mM_Menadione_.10_min.redo
1_mM_Menadione_.20_min._redo
1_mM_Menadione_.30_min._redo
1mM_Menadione_.40_min._redo
1_mM_Menadione_.50_min.redo
1_mM_Menadione_.80_min._redo
1_mM_Menadione_.105_min._redo
1_mM_Menadione_.120_min.redo
1_mM_Menadione_.160_min._redo
4.71 6.25 2.67 mitochondrion (732/88; 0.49E-003)
Golgi apparatus (90/17; 0.63E-003)
vesicle-med. Transp. (190/31; 0.84E-004)  
17 Heat_Shock_000_minutes_hs.2
Heat_Shock_000_minutes_hs.2.1
Heat_Shock_000_minutes_hs.2.2
37C_to_25C_shock_._15_min 37C_to_25C_shock_._30_min
37C_to_25C_shock_._45_min 37C_to_25C_shock_._60_min
37C_to_25C_shock_._90_min dtt_000_min_dtt.2
dtt_015_min_dtt.2 dtt_030_min_dtt.2
steady_state_21_dec_C_ct.2 steady_state_25_dec_C_ct.2
steady_state_29_dec_C_ct.2
5.33 #### 5.49 ribosome (368/145; 0.26E-007) nucleolus (325/138; 0.15E-009) ribosome biog & ass (271/121; 0.87E-011)
RNA metabolism (382/148; 0.14E-007)
protein biosynthesis (493/194 0.12E-010)
structural mol. act. (359/123; 0.11E-003)
RNA binding (268/96; 0.93E-004)
18 YP_fructose_vs_reference_pool_car.2
YP_glucose_vs_reference_pool_car.2
YP_mannose_vs_reference_pool_car.2
YP_sucrose_vs_reference_pool_car.2
2.12 0.31 0.32 mitochondrial membr (136/7; 0.59E-004)   
19 Hypo.osmotic_shock_._15_min
Hypo.osmotic_shock_._30_min
Hypo.osmotic_shock_._45_min
Hypo.osmotic_shock_._60_min
3.08 5.06 3.67 bud (59/6; 0.40E-003)
nucleolus (325/21; 0.525E-005)
ribosome biog & ass (271/24; 0.12E-007)
RNA metabolism (382/22; 0.86E-004
 
20 Heat_Shock_060_minutes_hs.2 NA NA NA    
21 17_deg_growth_ct.1 21_deg_growth_ct.1 25_deg_growth_ct.1
29_deg_growth_ct.1
1.67 1.54 -1.34    
22 steady_state_15_dec_C_ct.2 steady_state_17_dec_C_ct.2 0.51 -1.14 0.48    
23 2.5mM_DTT_005_min_dtt.1 2.5mM_DTT_015_min_dtt.1
2.5mM_DTT_030_min_dtt.1
0.03 1.28 0.32    
24 galactose_vs._reference_pool_car.1
glucose_vs._reference_pool_car.1
mannose_vs._reference_pool_car.1
raffinose_vs._reference_pool_car.1
sucrose_vs._reference_pool_car.1 steady_state_33_dec_C_ct.2
8.69 5.93 6.57 cell cortex (39/7; 0.97E-003)
cytoplasmic vesicle (52/11; 0.15E-004)
bud (59/10; 0.27E-003)
endomembrane syst (76/15; 0.21E-005)
cytokinesis (52/10; 0.25E-003)
nuclear org & biog (105/16; 0.20E-003)
vesicle-med transp (190/23; 0.55E-003)
helicase activity (71/13; 0.21E-004)
25 29C_to_33C_._30_minutes
29C_.1M_sorbitol_to_33C_._1M_sorbitol_._30_minutes
29C_.1M_sorbitol_to_33C_._.NO_sorbitol_._15_minute
29C_.1M_sorbitol_to_33C_._.NO_sorbitol_._30_minute
Hypo.osmotic_shock_._5_min steady.state_1M_sorbitol
0.39 2.96 3.27   DNA metabolism (221/8; 0.78E-003) DNA binding (146/7; 0.21E-003)
26 Heat_Shock_005_minutes_hs.2 NA NA NA    
  1. (a) GO terms discussed in the text are shown in bold. Together with each GO term, we show the number of genes corresponding to that term; the number of genes of that term in the cluster; and the corresponding P-value, according to the hipergeometric distribution.
  2. (b) NA: Data Not Available. No significant genes (according to the q-value cutoff) could be found.