Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91151	0.347
27DAP/17DAP	1.13933	1
39DAP/27DAP	0.96098	0.641
41DAP/39DAP	1.23262	0.914
42DAP/41DAP	1.35655	0.745
43DAP/42DAP	0.90842	0.775
47DAP/43DAP	1.03995	1
52DAP/47DAP	1.26074	0.624
57DAP/52DAP	0.96757	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94027	0.284
17DAP/reference	1.03401	0.138
27DAP/reference	1.02347	0.75
39DAP/reference	1.04558	0.162
41DAP/reference	1.08589	0.111
42DAP/reference	0.90653	0.012
43DAP/reference	1.0108	0.899
47DAP/reference	0.86268	0.001
52DAP/reference	0.91212	0.139
57DAP/reference	0.87488	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99528	0.847
27DAP/17DAP	1.01421	0.98
39DAP/27DAP	1.08101	0.512
41DAP/39DAP	1.00764	1
42DAP/41DAP	0.99923	0.887
43DAP/42DAP	1.05443	0.324
47DAP/43DAP	1.00999	1
52DAP/47DAP	0.98551	0.919
57DAP/52DAP	0.9817	0.745
57DAP/7DAP	1.12537	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83991	0.203
17DAP/reference	0.80858	0.018
27DAP/reference	0.73739	0.01
39DAP/reference	0.81168	0.015
41DAP/reference	0.85013	0.073
42DAP/reference	0.71682	0.011
43DAP/reference	0.73013	0.011
47DAP/reference	0.98618	1
52DAP/reference	0.73295	0.016
57DAP/reference	0.79165	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04736	0.545
17DAP/reference	1.05443	0.531
27DAP/reference	0.95478	0.423
39DAP/reference	0.95818	0.348
41DAP/reference	0.95415	0.177
42DAP/reference	0.89523	0.05
43DAP/reference	1.05955	0.509
47DAP/reference	0.92406	0.09
52DAP/reference	0.94881	0.203
57DAP/reference	1.10875	0.324

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99831	0.699
17DAP/reference	0.96231	0.579
27DAP/reference	0.81181	0.081
39DAP/reference	0.74307	0.025
41DAP/reference	0.91562	0.293
42DAP/reference	0.75093	0.025
43DAP/reference	0.76582	0.04
47DAP/reference	0.99487	0.667
52DAP/reference	0.77379	0.184
57DAP/reference	0.76771	0.06

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94361	1
26DAP/20DAP	0.90081	0.512
34DAP/26DAP	1.00665	1
51DAP/34DAP	0.8913	0.246
52DAP/51DAP	1.07692	0.431
53DAP/52DAP	1.00443	1
55DAP/53DAP	1.02222	0.834
57DAP/55DAP	0.96713	0.821
62DAP/57DAP	1.10856	0.185
68DAP/62DAP	0.78662	0.144
68DAP/14DAP	0.94755	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86932	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97343	0.715
Immature Eggplant/Mature Eggplant	1.16198	0.363
Ripe Pepper/Ripe Tomato	0.80501	1
Mature Eggplant/Ripe Tomato	2.47319	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04142	1
1-1-2/M82	0.80534	1
12-2/M82	1.07974	1
12-4/M82	1.12399
1-3/M82	0.87806
2-1-1/M82	1.21179	0.403
2-1/M82	N/A	N/A
2-6/M82	0.99256	1
3-2/M82	0.94851
4-1-1/M82	1.10164	0.968
4-1/M82	0.57195
4-3-2/M82	0.82996	0.458
4-3/M82	0.74939	0.611
5-3/M82	0.95837	0.447
6-2/M82	1.00457	1
6-3/M82	0.77496	0.982
7-1/M82	N/A	N/A
7-2/M82	1.15253	0.385
9-3-2/M82	0.72751	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74635	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.785
IL12-4/WTpooled	0.80077
IL1-4/WTpooled	0.72982
WT/WTpooled	1.11745	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.83585	0.497

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03104	0.914
DC3000/delta hrp 6h	1.10266	1
DC3000/delta hrp 12h	1.19097	1
DC3000/delta hrp 24h	1.00928	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05441	0.476
DC3000 delta B/DC3000 delta AB	0.94522	0.543

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98119	1
Exp 36h	0.99697	1
Exp 60h	1.10957	0.563

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.99302	1
Var 0h	0.69854	1
Var 12h I row2-row1	1.07988	0.204
Var 12h NI row2-row1	0.89587	0.546
Var 36h I row2-row1	0.9513	0.805
Var 36h NI row2-row1	0.90915	0.549
Var 60h I row2-row1	1.02301	1
Var 60h NI row2-row1	1.21853	0.904
Time course 0hI-0hNI	1.10052	0.63
Time course 12hI-12hNI	0.97121	0.814
Time course 36hI-36hNI	0.97136	0.36
Time course 60hI-60hNI	0.95606	0.646

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.9437	0.529
transgenic ySAMdc/azygous control (breaker)	0.65332	0.139
transgenic ySAMdc/azygous control (red)	0.88782	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0275	0.185

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86878	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73698	0.172
Manapal/WT (break)	0.65727	0.299
Manapal/WT (red)	0.87747	0.188