Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73075	0.26
27DAP/17DAP	1.45206	0.606
39DAP/27DAP	0.75982	0.447
41DAP/39DAP	1.13337	0.925
42DAP/41DAP	1.28365	0.962
43DAP/42DAP	1.22661	0.892
47DAP/43DAP	0.99106	0.754
52DAP/47DAP	1.54005	0.372
57DAP/52DAP	1.09257	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9803	0.589
17DAP/reference	0.766	0.074
27DAP/reference	0.97903	0.694
39DAP/reference	0.84536	0.085
41DAP/reference	0.72092	0.009
42DAP/reference	0.84967	0.069
43DAP/reference	0.85101	0.316
47DAP/reference	0.84931	0.032
52DAP/reference	0.82052	0.131
57DAP/reference	1.11748	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32712	0.326
27DAP/17DAP	1.19069	0.867
39DAP/27DAP	1.1941	0.691
41DAP/39DAP	2.4114	0.484
42DAP/41DAP	0.93028	0.679
43DAP/42DAP	1.04889	0.991
47DAP/43DAP	1.13117	0.817
52DAP/47DAP	0.97773	0.902
57DAP/52DAP	1.43607	0.543
57DAP/7DAP	1.04933

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95625	0.361
17DAP/reference	0.86262	0.144
27DAP/reference	0.82111	0.028
39DAP/reference	0.70551	0.013
41DAP/reference	0.6864	0.017
42DAP/reference	0.70537	0.031
43DAP/reference	0.82253	0.126
47DAP/reference	0.85081	0.168
52DAP/reference	0.84699	0.014
57DAP/reference	0.82873	0.034

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87914	0.248
17DAP/reference	0.76238	0.019
27DAP/reference	0.70418	0.036
39DAP/reference	0.80998	0.122
41DAP/reference	0.88109	0.067
42DAP/reference	0.78026	0.037
43DAP/reference	0.87502	0.243
47DAP/reference	0.79044	0.012
52DAP/reference	0.7857	0.005
57DAP/reference	0.8366	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89217	0.135
17DAP/reference	0.86921	0.165
27DAP/reference	1.11553	0.248
39DAP/reference	1.02048	0.819
41DAP/reference	0.8945	0.055
42DAP/reference	0.86356	0.134
43DAP/reference	0.99324	0.767
47DAP/reference	0.85129	0.038
52DAP/reference	1.8594	0.257
57DAP/reference	1.20639	0.223

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1168	0.966
26DAP/20DAP	1.79631
34DAP/26DAP	1.4385	1
51DAP/34DAP	1.06487	0.917
52DAP/51DAP	1.26054	0.626
53DAP/52DAP	0.70147	0.15
55DAP/53DAP	1.37185	0.696
57DAP/55DAP	1.09476	0.875
62DAP/57DAP	1.18719	0.935
68DAP/62DAP	1.91444	0.126
68DAP/14DAP	2.21412	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87347	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.52885	0.031
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.63017

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.65413
12-2/M82	N/A	N/A
12-4/M82	0.71435	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.8396
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.95674
4-3/M82	1.06347
5-3/M82	1.25947	1
6-2/M82	0.94356
6-3/M82	0.98483	1
7-1/M82	1.08177
7-2/M82	1.17323
9-3-2/M82	1.4418

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.67402	0.277
IL2-6/WTpooled	0.9832	1
IL7-5/WTpooled	1.00321	1
IL7-3/WTpooled	1.07896	1
IL12-4/WTpooled	1.2451	0.737
IL1-4/WTpooled	1.12993	1
WT/WTpooled	0.98062	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	1.23048	0.148

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98553	1
DC3000/delta hrp 6h	0.97436	0.95
DC3000/delta hrp 12h	1.33777	1
DC3000/delta hrp 24h	1.04861	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.95286	0.873

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99747	1
Exp 36h	0.69969	0.406
Exp 60h	0.9097	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98572	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.14019	0.506
Var 12h NI row2-row1	2.49782	0.649
Var 36h I row2-row1	0.84799	1
Var 36h NI row2-row1	1.11081	1
Var 60h I row2-row1	0.78982	0.306
Var 60h NI row2-row1	0.80733	1
Time course 0hI-0hNI	1.17429	0.799
Time course 12hI-12hNI	3.74724	0.004
Time course 36hI-36hNI	2.01342	0.008
Time course 60hI-60hNI	16.23	0.008

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)	4.22184	0.212
transgenic ySAMdc/azygous control (breaker)	0.29828	0.134
transgenic ySAMdc/azygous control (red)	1.59673	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9141	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.34742	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.59752	1
Manapal/WT (break)	1.48307	1
Manapal/WT (red)	0.74456	0.216