Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.4.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2031	0.414
27DAP/17DAP	1.0721	1
39DAP/27DAP	0.83768	0.529
41DAP/39DAP	0.83215	0.494
42DAP/41DAP	0.91928	0.774
43DAP/42DAP	1.12374	0.985
47DAP/43DAP	0.88867	0.628
52DAP/47DAP	1.19448	0.791
57DAP/52DAP	0.97758	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84785	0.045
17DAP/reference	0.88685	0.085
27DAP/reference	0.90075	0.141
39DAP/reference	1.00848	0.889
41DAP/reference	0.99637	1
42DAP/reference	0.85581	0.02
43DAP/reference	0.865	0.021
47DAP/reference	0.95994	0.224
52DAP/reference	1.03679	0.84
57DAP/reference	1.11105	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96503	0.595
27DAP/17DAP	1.04765	0.887
39DAP/27DAP	1.0038	1
41DAP/39DAP	1.06667	0.807
42DAP/41DAP	0.95753	0.679
43DAP/42DAP	1.02625	0.585
47DAP/43DAP	1.0255	0.969
52DAP/47DAP	1.05984	0.776
57DAP/52DAP	0.95682	0.646
57DAP/7DAP	0.96555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94436	0.445
17DAP/reference	0.8098	0.056
27DAP/reference	0.83462	0.048
39DAP/reference	1.09016	0.909
41DAP/reference	1.03464	0.864
42DAP/reference	0.92767	0.289
43DAP/reference	0.97236	0.459
47DAP/reference	0.83819	0.293
52DAP/reference	0.91956	0.278
57DAP/reference	0.86049	0.207

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91679	0.268
17DAP/reference	0.8204	0.036
27DAP/reference	1.01594	0.79
39DAP/reference	0.97437	0.485
41DAP/reference	1.00178	0.702
42DAP/reference	1.09088	0.094
43DAP/reference	1.39666	0.356
47DAP/reference	1.06165	0.388
52DAP/reference	0.97283	0.433
57DAP/reference	0.78766	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79753	0.119
17DAP/reference	1.04169	0.924
27DAP/reference	0.8067	0.113
39DAP/reference	0.83491	0.122
41DAP/reference	0.82596	0.185
42DAP/reference	0.84274	0.22
43DAP/reference	0.98097	0.614
47DAP/reference	1.02931	1
52DAP/reference	0.79735	0.145
57DAP/reference	1.3195	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04148	0.966
26DAP/20DAP	1.14825	0.762
34DAP/26DAP	1.04276	1
51DAP/34DAP	1.06847	0.677
52DAP/51DAP	0.94107	1
53DAP/52DAP	0.98889	0.929
55DAP/53DAP	1.08428	0.813
57DAP/55DAP	0.91192	0.619
62DAP/57DAP	0.98942	0.994
68DAP/62DAP	1.44829	0.155
68DAP/14DAP	1.64088	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03089	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.647	N/A
Immature Eggplant/Mature Eggplant	0.90804	0.808
Ripe Pepper/Ripe Tomato	1.34404	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.94955	N/A
12-4/M82	1.36298	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.00856	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	N/A	N/A
7-2/M82	0.83963	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09973	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.01181	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.82305	N/A
IL1-4/WTpooled	1.08369	1
WT/WTpooled	0.99335	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	1.29758	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98264	1
DC3000/delta hrp 6h	1.13151	1
DC3000/delta hrp 12h	0.94016	1
DC3000/delta hrp 24h	0.983	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09046	1
DC3000 delta B/DC3000 delta AB	0.89125	0.674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96263	1
Exp 36h	0.80538	0.699
Exp 60h	1.24569	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97023	1
Var 0h	0.51491	0.98
Var 12h I row2-row1	1.04696	0.324
Var 12h NI row2-row1	1.02566	1
Var 36h I row2-row1	1.10729	0.742
Var 36h NI row2-row1	1.11159	1
Var 60h I row2-row1	1.07804	1
Var 60h NI row2-row1	1.08352	0.904
Time course 0hI-0hNI	1.01221	0.852
Time course 12hI-12hNI	0.97813	0.841
Time course 36hI-36hNI	1.02094	0.975
Time course 60hI-60hNI	1.23404	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)	1.14436	0.397
transgenic ySAMdc/azygous control (breaker)	0.64122	0.142
transgenic ySAMdc/azygous control (red)	0.94089	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05759	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61691	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.50459	1
Manapal/WT (break)	1.18953	0.381
Manapal/WT (red)	1.07992	1