Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93363	0.617
27DAP/17DAP	0.87005	0.839
39DAP/27DAP	0.67611	0.216
41DAP/39DAP	0.86892	0.59
42DAP/41DAP	0.90499	1
43DAP/42DAP	0.99035	0.937
47DAP/43DAP	1.05821	0.999
52DAP/47DAP	0.99411	0.948
57DAP/52DAP	1.14031	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01121	1
17DAP/reference	1.06383	0.122
27DAP/reference	1.05447	0.205
39DAP/reference	1.01298	0.76
41DAP/reference	1.01995	0.714
42DAP/reference	1.0078	1
43DAP/reference	1.03551	0.547
47DAP/reference	0.99374	0.602
52DAP/reference	0.89205	0.099
57DAP/reference	0.93852	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94333	0.289
27DAP/17DAP	1.00458	0.995
39DAP/27DAP	1.00814	0.824
41DAP/39DAP	0.97507	0.934
42DAP/41DAP	0.99307	0.892
43DAP/42DAP	1.02217	0.746
47DAP/43DAP	0.95172	0.339
52DAP/47DAP	0.94684	0.694
57DAP/52DAP	0.97385	0.668
57DAP/7DAP	0.93952	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07396	0.638
17DAP/reference	0.94712	0.338
27DAP/reference	0.90652	0.185
39DAP/reference	0.83592	0.083
41DAP/reference	0.95686	0.412
42DAP/reference	0.77042	0.016
43DAP/reference	0.90336	0.192
47DAP/reference	0.9278	0.293
52DAP/reference	0.9197	0.15
57DAP/reference	1.21356	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97874	0.655
17DAP/reference	1.00082	0.873
27DAP/reference	0.92055	0.22
39DAP/reference	0.96005	0.381
41DAP/reference	0.92413	0.098
42DAP/reference	0.98306	0.433
43DAP/reference	0.91178	0.269
47DAP/reference	0.98588	0.512
52DAP/reference	0.95198	0.22
57DAP/reference	1.02826	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98729	0.607
17DAP/reference	1.00699	1
27DAP/reference	0.94304	0.594
39DAP/reference	0.96264	0.643
41DAP/reference	1.22848	0.455
42DAP/reference	1.14019	0.848
43DAP/reference	1.02967	0.973
47DAP/reference	0.96914	0.421
52DAP/reference	0.85352	0.232
57DAP/reference	1.0329	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0111	0.966
26DAP/20DAP	0.92834	1
34DAP/26DAP	1.0081	1
51DAP/34DAP	0.8896	0.174
52DAP/51DAP	0.99993	1
53DAP/52DAP	1.0662	0.623
55DAP/53DAP	1.2014	N/A
57DAP/55DAP	1.01419	0.986
62DAP/57DAP	0.95874	0.994
68DAP/62DAP	0.93067	0.747
68DAP/14DAP	1.07066	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.935	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.37155	0.075
Mature Green Tomato/Ripe Tomato	0.63675	0.132
Immature Eggplant/Mature Eggplant	1.28258	0.248
Ripe Pepper/Ripe Tomato	1.1197	1
Mature Eggplant/Ripe Tomato	0.95126	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.76659	0.651
1-1-2/M82	0.95696	1
12-2/M82	0.95152	0.955
12-4/M82	1.01158	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.86039	N/A
2-1/M82	N/A	N/A
2-6/M82	0.90241	N/A
3-2/M82	0.83617	N/A
4-1-1/M82	1.09374	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.95258	N/A
5-3/M82	1.23785	1
6-2/M82	0.79812	1
6-3/M82	1.00401	1
7-1/M82	1.00994	N/A
7-2/M82	0.89765	N/A
9-3-2/M82	0.95357	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85475	N/A
IL2-6/WTpooled	1.52629	N/A
IL7-5/WTpooled	1.96208	N/A
IL7-3/WTpooled	1.05598	1
IL12-4/WTpooled	0.88453	0.71
IL1-4/WTpooled	1.16006	1
WT/WTpooled	0.94526	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	0.95357	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96327	1
DC3000/delta hrp 6h	0.80523	N/A
DC3000/delta hrp 12h	0.94357	1
DC3000/delta hrp 24h	1.11516	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16031	0.145
DC3000 delta B/DC3000 delta AB	1.00598	0.761

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98662	1
Exp 36h	1.08014	1
Exp 60h	1.00146	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99357	1
Var 0h	0.91565	0.332
Var 12h I row2-row1	1.13371	0.187
Var 12h NI row2-row1	1.02995	1
Var 36h I row2-row1	0.95782	1
Var 36h NI row2-row1	0.93236	0.743
Var 60h I row2-row1	1.1201	1
Var 60h NI row2-row1	1.15348	0.904
Time course 0hI-0hNI	1.02713	0.852
Time course 12hI-12hNI	1.00561	0.888
Time course 36hI-36hNI	1.02357	0.355
Time course 60hI-60hNI	1.1607	0.013

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)	0.95224	0.314
transgenic ySAMdc/azygous control (breaker)	0.95667	1
transgenic ySAMdc/azygous control (red)	1.1631	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00449	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9615	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75433	0.172
Manapal/WT (break)	1.00148	1
Manapal/WT (red)	1.65691	0.413