Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71631	0.144
27DAP/17DAP	0.7407	0.217
39DAP/27DAP	3.1677	0.033
41DAP/39DAP	0.7404	0.116
42DAP/41DAP	1.12038	0.992
43DAP/42DAP	1.58598	0.918
47DAP/43DAP	0.5589	0.055
52DAP/47DAP	0.74479	0.31
57DAP/52DAP	1.01309	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38169	0.17
17DAP/reference	0.75144	0.022
27DAP/reference	0.86182	0.163
39DAP/reference	0.98511	0.734
41DAP/reference	0.79098	0.085
42DAP/reference	1.68778	0.001
43DAP/reference	1.77499	0.007
47DAP/reference	1.1549	0.306
52DAP/reference	0.70053	0.017
57DAP/reference	1.16426	0.173

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.38509	0.034
27DAP/17DAP	1.3716	0.044
39DAP/27DAP	1.04163	0.793
41DAP/39DAP	0.99115	0.945
42DAP/41DAP	1.04258	0.864
43DAP/42DAP	1.17849	0.382
47DAP/43DAP	1.25582	0.331
52DAP/47DAP	0.5998	0.089
57DAP/52DAP	0.97098	0.73
57DAP/7DAP	0.33752	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.09164	0.024
17DAP/reference	1.06972	0.399
27DAP/reference	2.46729	0.006
39DAP/reference	1.58537	0.018
41DAP/reference	1.99057	0.026
42DAP/reference	2.90162	0.007
43DAP/reference	3.21826	0.007
47DAP/reference	3.93665	0.014
52DAP/reference	3.78051	0.007
57DAP/reference	1.73568	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38242	0.162
17DAP/reference	0.78777	0.019
27DAP/reference	1.44572	0.029
39DAP/reference	1.0585	0.67
41DAP/reference	0.92458	0.127
42DAP/reference	1.27357	0.056
43DAP/reference	1.05891	0.657
47DAP/reference	1.82382	0.042
52DAP/reference	0.65499	0.003
57DAP/reference	1.07042	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.1278	0.021
17DAP/reference	0.82536	0.186
27DAP/reference	1.51611	0.027
39DAP/reference	2.47434	0.006
41DAP/reference	1.6987	0.007
42DAP/reference	3.49373	0.007
43DAP/reference	3.384	0.007
47DAP/reference	1.25156	0.019
52DAP/reference	1.6095	0.081
57DAP/reference	0.81688	0.098

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.81265	0.773
26DAP/20DAP	0.93103	1
34DAP/26DAP	0.9168	0.322
51DAP/34DAP	0.53079	0.049
52DAP/51DAP	0.9877	1
53DAP/52DAP	0.68974	0.056
55DAP/53DAP	0.4306	0.016
57DAP/55DAP	1.01491	0.97
62DAP/57DAP	0.91081	0.681
68DAP/62DAP	0.89872	0.722
68DAP/14DAP	1.16692	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30663	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.21204	0.058
Mature Green Tomato/Ripe Tomato	0.97075	0.66
Immature Eggplant/Mature Eggplant	2.1857	0.05
Ripe Pepper/Ripe Tomato	0.12238	0.224
Mature Eggplant/Ripe Tomato	0.55555	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.33778	0.536
1-1-2/M82	1.76226	1
12-2/M82	0.97052	0.955
12-4/M82	2.03025	1
1-3/M82	2.80616	1
2-1-1/M82	1.13538	0.689
2-1/M82	0.95989	1
2-6/M82	1.79901	0.452
3-2/M82	1.08418	0.717
4-1-1/M82	1.89467	1
4-1/M82	3.57356	0.853
4-3-2/M82	2.78312	0.246
4-3/M82	1.1593	1
5-3/M82	0.99079	1
6-2/M82	1.80465	1
6-3/M82	1.08622	1
7-1/M82	0.98104	1
7-2/M82	1.09809	1
9-3-2/M82	2.37648	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11612	0.277
IL2-6/WTpooled	1.08133	0.659
IL7-5/WTpooled	1.08268	0.75
IL7-3/WTpooled	0.98599	1
IL12-4/WTpooled	1.01483	1
IL1-4/WTpooled	0.98643	1
WT/WTpooled	0.99333	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	1.12155	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.23536	0.875
DC3000/delta hrp 6h	1.24696	0.609
DC3000/delta hrp 12h	1.09482	1
DC3000/delta hrp 24h	2.58765	0.026

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60752	0.024
DC3000 delta B/DC3000 delta AB	0.64522	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01493	1
Var 0h	1.12904	1
Var 12h I row2-row1	0.95553	0.77
Var 12h NI row2-row1	0.96839	0.906
Var 36h I row2-row1	1.24924	0.298
Var 36h NI row2-row1	0.96591	0.706
Var 60h I row2-row1	0.87176	0.306
Var 60h NI row2-row1	0.92947	1
Time course 0hI-0hNI	1.02966	0.799
Time course 12hI-12hNI	1.03024	0.85
Time course 36hI-36hNI	1.27344	0.008
Time course 60hI-60hNI	1.09486	1

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)	0.84967	0.286
transgenic ySAMdc/azygous control (breaker)	0.74356	0.251
transgenic ySAMdc/azygous control (red)	1.35443	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97386	0.201

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88041	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04654	0.307
Manapal/WT (break)	0.81343	0.333
Manapal/WT (red)	1.09174	0.164