Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89574	0.522
27DAP/17DAP	1.19369	0.825
39DAP/27DAP	1.4242	0.344
41DAP/39DAP	1.01244	0.941
42DAP/41DAP	1.25771	0.691
43DAP/42DAP	1.41321	0.424
47DAP/43DAP	0.93185	0.729
52DAP/47DAP	1.59517	0.372
57DAP/52DAP	0.84534	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75559	0.075
17DAP/reference	0.68339	0.024
27DAP/reference	0.62017	0.015
39DAP/reference	0.88585	0.298
41DAP/reference	0.64331	0.012
42DAP/reference	1.3718	0.005
43DAP/reference	2.149	0.007
47DAP/reference	2.07883	0.001
52DAP/reference	1.13085	0.766
57DAP/reference	1.16567	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39249	0.036
27DAP/17DAP	0.92432	0.537
39DAP/27DAP	1.21442	0.173
41DAP/39DAP	0.86198	0.42
42DAP/41DAP	1.22583	0.028
43DAP/42DAP	1.4384	0.017
47DAP/43DAP	1.09177	0.593
52DAP/47DAP	1.02352	1
57DAP/52DAP	1.273	0.244
57DAP/7DAP	2.27415	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03157	0.857
17DAP/reference	0.70609	0.02
27DAP/reference	0.71306	0.01
39DAP/reference	0.81953	0.049
41DAP/reference	0.73443	0.018
42DAP/reference	0.80208	0.032
43DAP/reference	1.13826	0.457
47DAP/reference	1.31269	0.07
52DAP/reference	0.8247	0.072
57DAP/reference	0.70197	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56493	0.005
17DAP/reference	0.54368	0.004
27DAP/reference	0.83904	0.139
39DAP/reference	0.78276	0.033
41DAP/reference	0.64507	0.012
42DAP/reference	0.72906	0.025
43DAP/reference	0.53504	0.003
47DAP/reference	0.91404	0.261
52DAP/reference	0.40967	0.004
57DAP/reference	0.60128	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92201	0.311
17DAP/reference	0.60348	0.009
27DAP/reference	0.6807	0.025
39DAP/reference	0.97615	0.544
41DAP/reference	0.87133	0.148
42DAP/reference	1.59791	0.03
43DAP/reference	2.40881	0.006
47DAP/reference	1.04462	0.63
52DAP/reference	1.58157	0.033
57DAP/reference	0.91696	0.278

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97904	1
26DAP/20DAP	1.10787	0.941
34DAP/26DAP	0.95776	0.92
51DAP/34DAP	1.58233	0.06
52DAP/51DAP	0.86193	1
53DAP/52DAP	3.29915	0.041
55DAP/53DAP	0.87726	0.159
57DAP/55DAP	0.8906	0.496
62DAP/57DAP	0.40177	0.007
68DAP/62DAP	0.80584	0.429
68DAP/14DAP	0.97585

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.80942	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.28486	0.068
Mature Green Tomato/Ripe Tomato	0.20094	0.027
Immature Eggplant/Mature Eggplant	2.45911	0.05
Ripe Pepper/Ripe Tomato	0.54965	0.224
Mature Eggplant/Ripe Tomato	0.11643	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.152	0.877
1-1-2/M82	1.19231	1
12-2/M82	0.9335	0.955
12-4/M82	1.1913	1
1-3/M82	2.65015	0.277
2-1-1/M82	1.05093	0.764
2-1/M82	1.10775	1
2-6/M82	1.09834	1
3-2/M82	0.97906	1
4-1-1/M82	0.9104	1
4-1/M82	1.11665	1
4-3-2/M82	1.22938	0.262
4-3/M82	0.91448	0.72
5-3/M82	1.22432	0.467
6-2/M82	1.65844	1
6-3/M82	0.94016	1
7-1/M82	0.95963	1
7-2/M82	1.45741
9-3-2/M82	1.29414	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91482	1
IL2-6/WTpooled	1.004	1
IL7-5/WTpooled	0.94363
IL7-3/WTpooled	1.07883	1
IL12-4/WTpooled	1.00872	1
IL1-4/WTpooled	0.91202	0.834
WT/WTpooled	1.0082	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	1.24619	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04818	0.921
DC3000/delta hrp 6h	1.37433	1
DC3000/delta hrp 12h	1.0467	1
DC3000/delta hrp 24h	0.8308	0.096

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.979	1
DC3000 delta B/DC3000 delta AB	1.4387	0.115

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20988	1
Exp 36h	1.07551	1
Exp 60h	1.42258	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09737	1
Var 0h	1.09601	0.594
Var 12h I row2-row1	0.9111	0.565
Var 12h NI row2-row1	1.10425	0.34
Var 36h I row2-row1	1.03147	1
Var 36h NI row2-row1	0.83029	0.421
Var 60h I row2-row1	0.78837	0.306
Var 60h NI row2-row1	0.8074	0.572
Time course 0hI-0hNI	1.02552	0.867
Time course 12hI-12hNI	0.97762	0.841
Time course 36hI-36hNI	1.35304	0.009
Time course 60hI-60hNI	3.18599	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)	1.06057	0.654
transgenic ySAMdc/azygous control (breaker)	0.84483	0.173
transgenic ySAMdc/azygous control (red)	1.03244	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.8034	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87464	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.52089	0.09
Manapal/WT (break)	1.03532	1
Manapal/WT (red)	0.68207	0.181