Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.63029	0.359
27DAP/17DAP	1.13571	0.92
39DAP/27DAP	3.10972	0.219
41DAP/39DAP	1.56931	0.437
42DAP/41DAP	3.11997	0.022
43DAP/42DAP	1.64997	0.956
47DAP/43DAP	2.14924	0.201
52DAP/47DAP	0.90975	0.702
57DAP/52DAP	1.84688	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24025	0.132
17DAP/reference	1.06835	0.565
27DAP/reference	1.12502	0.375
39DAP/reference	1.45774	0.014
41DAP/reference	1.36548	0.019
42DAP/reference	1.83888	0.001
43DAP/reference	1.82573	0.008
47DAP/reference	3.19473	0.001
52DAP/reference	2.128	0.01
57DAP/reference	2.05204	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21933	0.708
27DAP/17DAP	1.20069	0.65
39DAP/27DAP	1.90873	0.078
41DAP/39DAP	0.64265	0.033
42DAP/41DAP	1.12953	0.927
43DAP/42DAP	3.24849	0.016
47DAP/43DAP	1.28	0.286
52DAP/47DAP	1.31906	0.386
57DAP/52DAP	1.02753	0.852
57DAP/7DAP	2.12127	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98951	0.682
17DAP/reference	0.87206	0.039
27DAP/reference	0.85742	0.146
39DAP/reference	0.84034	0.109
41DAP/reference	0.98485	0.589
42DAP/reference	0.91648	0.136
43DAP/reference	1.03271	1
47DAP/reference	1.0618	1
52DAP/reference	1.10539	0.781
57DAP/reference	0.90598	0.118

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90713	0.503
17DAP/reference	1.37098	0.043
27DAP/reference	1.37191	0.126
39DAP/reference	1.36181	0.011
41DAP/reference	1.20132	0.138
42DAP/reference	1.32125	0.027
43DAP/reference	1.12244	0.875
47DAP/reference	1.34719	0.029
52DAP/reference	1.03227	1
57DAP/reference	0.93144	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82092	0.135
17DAP/reference	1.23609	0.137
27DAP/reference	1.07756	1
39DAP/reference	0.87252	0.271
41DAP/reference	1.32447	0.213
42DAP/reference	1.4799	0.134
43DAP/reference	1.92794	0.017
47DAP/reference	2.17041	0.005
52DAP/reference	1.25663	0.19
57DAP/reference	1.8715	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89578	1
26DAP/20DAP	1.08222	1
34DAP/26DAP	1.17734	1
51DAP/34DAP	1.01941	0.893
52DAP/51DAP	1.28449	0.848
53DAP/52DAP	1.12348	0.858
55DAP/53DAP	0.90404	0.619
57DAP/55DAP	0.94651	0.76
62DAP/57DAP	0.95748	0.871
68DAP/62DAP	1.17961	0.878
68DAP/14DAP	1.10946	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	8.96528	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.092	0.017
Immature Eggplant/Mature Eggplant	1.23575	0.15
Ripe Pepper/Ripe Tomato	0.07929	0.224
Mature Eggplant/Ripe Tomato	0.04371

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.55178
12-2/M82	N/A	N/A
12-4/M82	2.45359
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	N/A	N/A
3-2/M82	1.09357	0.84
4-1-1/M82	N/A	N/A
4-1/M82	1.495
4-3-2/M82	1.51768	0.508
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.06364
7-2/M82	N/A	N/A
9-3-2/M82	1.66165

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98809	1
IL2-6/WTpooled	1.04045	1
IL7-5/WTpooled	0.89215	1
IL7-3/WTpooled	0.88345	0.418
IL12-4/WTpooled	0.9706	1
IL1-4/WTpooled	0.87135	0.699
WT/WTpooled	1.1166	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	1.36737	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21456
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.80735
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.5208
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	1.00295	1
Exp 36h	N/A	N/A
Exp 60h	0.85194	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9043	1
Var 0h	1.05116	0.98
Var 12h I row2-row1	0.95337	0.948
Var 12h NI row2-row1	1.01303	1
Var 36h I row2-row1	0.88563	0.438
Var 36h NI row2-row1	0.91348	0.743
Var 60h I row2-row1	1.06737	0.407
Var 60h NI row2-row1	1.11319	0.904
Time course 0hI-0hNI	0.97123	0.87
Time course 12hI-12hNI	1.04204	0.818
Time course 36hI-36hNI	0.97696	0.524
Time course 60hI-60hNI	0.72596	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)	0.82204	0.348
transgenic ySAMdc/azygous control (breaker)	1.13037	1
transgenic ySAMdc/azygous control (red)	0.9703	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69696	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.2765	1
Manapal/WT (red)	N/A	N/A