Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90438	0.586
27DAP/17DAP	1.14472	0.841
39DAP/27DAP	1.15929	0.693
41DAP/39DAP	1.11695	0.545
42DAP/41DAP	1.22391	0.722
43DAP/42DAP	0.89082	0.741
47DAP/43DAP	1.27594	0.502
52DAP/47DAP	0.87928	0.662
57DAP/52DAP	0.93584	0.899

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99289	0.707
17DAP/reference	1.0543	0.294
27DAP/reference	0.95053	0.369
39DAP/reference	0.99166	0.901
41DAP/reference	0.98553	0.667
42DAP/reference	1.06282	0.166
43DAP/reference	0.96689	0.464
47DAP/reference	0.87825	0.071
52DAP/reference	0.86245	0.102
57DAP/reference	0.83027	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21905	0.048
27DAP/17DAP	0.8819	0.206
39DAP/27DAP	1.11501	0.331
41DAP/39DAP	1.00177	1
42DAP/41DAP	0.95605	0.666
43DAP/42DAP	0.93692	0.28
47DAP/43DAP	1.0551	0.772
52DAP/47DAP	0.97458	0.902
57DAP/52DAP	0.927	0.348
57DAP/7DAP	1.44975	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99615	0.758
17DAP/reference	0.77074	0.018
27DAP/reference	0.84016	0.033
39DAP/reference	0.93944	0.17
41DAP/reference	0.96442	0.375
42DAP/reference	0.85541	0.031
43DAP/reference	0.77972	0.02
47DAP/reference	0.89305	0.128
52DAP/reference	0.95356	0.332
57DAP/reference	0.95238	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.996	0.884
17DAP/reference	0.97098	0.523
27DAP/reference	1.00982	1
39DAP/reference	1.0901	1
41DAP/reference	1.08063	0.573
42DAP/reference	1.05563	0.915
43DAP/reference	1.08469	0.457
47DAP/reference	1.04811	0.24
52DAP/reference	0.94385	0.351
57DAP/reference	0.81188	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84317	0.087
17DAP/reference	0.98131	0.668
27DAP/reference	0.71372	0.023
39DAP/reference	0.698	0.008
41DAP/reference	0.8668	0.035
42DAP/reference	0.78366	0.015
43DAP/reference	0.79042	0.052
47DAP/reference	0.98298	0.558
52DAP/reference	0.70696	0.123
57DAP/reference	0.71763	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09809	0.966
26DAP/20DAP	0.96138	1
34DAP/26DAP	0.96027	0.898
51DAP/34DAP	0.93018	0.563
52DAP/51DAP	1.15707	0.446
53DAP/52DAP	1.13872	0.24
55DAP/53DAP	1.02827	0.991
57DAP/55DAP	1.06173	0.969
62DAP/57DAP	1.1711	0.303
68DAP/62DAP	0.77605	0.177
68DAP/14DAP	0.92804	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97818	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65117	0.165
Mature Green Tomato/Ripe Tomato	1.04711	0.881
Immature Eggplant/Mature Eggplant	1.61931	0.05
Ripe Pepper/Ripe Tomato	1.28062	0.256
Mature Eggplant/Ripe Tomato	1.40889	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17142
1-1-2/M82	N/A	N/A
12-2/M82	1.18396
12-4/M82	1.18277	1
1-3/M82	N/A	N/A
2-1-1/M82	0.89902
2-1/M82	N/A	N/A
2-6/M82	0.85704	1
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	0.73212
4-3/M82	N/A	N/A
5-3/M82	0.94632	1
6-2/M82	N/A	N/A
6-3/M82	1.22193	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.86805

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.78896	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0858
IL12-4/WTpooled	0.67021	0.484
IL1-4/WTpooled	1.27088
WT/WTpooled	1.05388	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	0.90974	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.31878	0.774
DC3000/delta hrp 6h	1.03454	1
DC3000/delta hrp 12h	1.17359	1
DC3000/delta hrp 24h	1.207	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71644	0.029
DC3000 delta B/DC3000 delta AB	0.7385	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20611	1
Exp 36h	1.08394	0.409
Exp 60h	1.17902	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05774	1
Var 0h	1.02859	0.98
Var 12h I row2-row1	0.89892	0.856
Var 12h NI row2-row1	1.16109	0.649
Var 36h I row2-row1	1.13181	0.908
Var 36h NI row2-row1	1.49271	0.276
Var 60h I row2-row1	0.83701	0.306
Var 60h NI row2-row1	0.8177	0.69
Time course 0hI-0hNI	0.80916	0.051
Time course 12hI-12hNI	1.04	0.867
Time course 36hI-36hNI	0.9976	0.621
Time course 60hI-60hNI	0.80507	0.007

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)	0.75693	0.286
transgenic ySAMdc/azygous control (breaker)	0.66876	0.139
transgenic ySAMdc/azygous control (red)	0.93575	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.15277	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8283	1
Manapal/WT (break)	0.88709	1
Manapal/WT (red)	0.78226	0.229