Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.794	0.285
27DAP/17DAP	1.09915	0.866
39DAP/27DAP	1.15253	0.789
41DAP/39DAP	0.9313	0.717
42DAP/41DAP	1.0321	0.992
43DAP/42DAP	0.87243	0.71
47DAP/43DAP	1.03163	0.965
52DAP/47DAP	1.40642	0.444
57DAP/52DAP	1.06196	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83138	0.036
17DAP/reference	1.0673	0.33
27DAP/reference	0.96246	0.668
39DAP/reference	1.0085	0.92
41DAP/reference	1.12772	0.338
42DAP/reference	0.888	0.011
43DAP/reference	1.0978	0.126
47DAP/reference	0.90932	0.106
52DAP/reference	1.23977	0.229
57DAP/reference	0.97145	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94825	0.56
27DAP/17DAP	0.91741	0.854
39DAP/27DAP	0.98558	0.953
41DAP/39DAP	1.00301	1
42DAP/41DAP	0.84455	0.303
43DAP/42DAP	1.04542	0.788
47DAP/43DAP	1.10778	0.713
52DAP/47DAP	1.06905	0.945
57DAP/52DAP	1.41621	0.104
57DAP/7DAP	2.26926	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06818	0.927
17DAP/reference	1.27323	0.123
27DAP/reference	1.38949	0.023
39DAP/reference	1.22626	0.029
41DAP/reference	1.68306	0.011
42DAP/reference	1.4813	0.018
43DAP/reference	1.40439	0.027
47DAP/reference	1.22513	0.214
52DAP/reference	1.32115	0.092
57DAP/reference	1.26219	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04975	0.732
17DAP/reference	0.74443	0.006
27DAP/reference	0.95737	0.352
39DAP/reference	0.79751
41DAP/reference	1.08433	1
42DAP/reference	0.94655	0.321
43DAP/reference	0.77932	0.132
47DAP/reference	0.76565	0.053
52DAP/reference	0.32442
57DAP/reference	N/A	N/A

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22309	0.043
17DAP/reference	1.17624	0.279
27DAP/reference	0.96683	0.357
39DAP/reference	1.03046	0.792
41DAP/reference	1.19507	0.112
42DAP/reference	0.91855	0.361
43DAP/reference	1.01488	0.796
47DAP/reference	1.21427	0.171
52DAP/reference	1.42025	0.664
57DAP/reference	0.81701	0.152

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91755	1
26DAP/20DAP	1.16721	0.647
34DAP/26DAP	1.55097	0.819
51DAP/34DAP	1.61195	0.055
52DAP/51DAP	1.00207	1
53DAP/52DAP	0.87026	0.595
55DAP/53DAP	1.15506	0.382
57DAP/55DAP	0.79436	0.271
62DAP/57DAP	1.18149	0.767
68DAP/62DAP	1.13153	0.869
68DAP/14DAP	1.07746	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33098	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74644
Mature Green Tomato/Ripe Tomato	0.58325	0.06
Immature Eggplant/Mature Eggplant	2.55466	0.116
Ripe Pepper/Ripe Tomato	0.59938	0.293
Mature Eggplant/Ripe Tomato	0.62548	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75951
1-1-2/M82	1.04958
12-2/M82	1.08595
12-4/M82	0.82464
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.83113
3-2/M82	0.97901	0.752
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.68074
4-3/M82	1.04289	1
5-3/M82	1.13199	0.572
6-2/M82	N/A	N/A
6-3/M82	0.95138
7-1/M82	0.97744
7-2/M82	0.85384
9-3-2/M82	0.67292

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	4.28682
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.30294
IL1-4/WTpooled	1.42716
WT/WTpooled	0.92175	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	1.10526	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01225	1
DC3000/delta hrp 6h	1.13693	1
DC3000/delta hrp 12h	0.96897	1
DC3000/delta hrp 24h	1.28783	0.103

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03065	1
Exp 36h	1.05098	0.693
Exp 60h	1.13525	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.00493	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.14286	0.482
transgenic ySAMdc/azygous control (breaker)	0.6163	0.131
transgenic ySAMdc/azygous control (red)	1.13497	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01517	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71447	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26767	0.105
Manapal/WT (break)	0.99683	1
Manapal/WT (red)	1.2034	0.164