Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13952	0.838
27DAP/17DAP	0.6899	0.244
39DAP/27DAP	0.71995	0.286
41DAP/39DAP	1.13114	0.685
42DAP/41DAP	1.29831	0.877
43DAP/42DAP	1.0646	1
47DAP/43DAP	0.95567	0.804
52DAP/47DAP	0.65897	0.185
57DAP/52DAP	1.24489	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97068	0.489
17DAP/reference	0.81248	0.097
27DAP/reference	0.88639	0.147
39DAP/reference	0.67605	0.018
41DAP/reference	0.67032	0.018
42DAP/reference	0.87302	0.03
43DAP/reference	0.86413	0.163
47DAP/reference	0.9	0.077
52DAP/reference	1.02375	0.668
57DAP/reference	1.06632	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82088	0.323
27DAP/17DAP	1.70605	0.35
39DAP/27DAP	0.98106	1
41DAP/39DAP	1.03181	0.914
42DAP/41DAP	1.31942	0.021
43DAP/42DAP	0.92395	0.538
47DAP/43DAP	1.41362	0.456
52DAP/47DAP	0.94408	0.797
57DAP/52DAP	0.79663	0.201
57DAP/7DAP	1.058	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11442	0.491
17DAP/reference	1.267	0.199
27DAP/reference	1.18513	0.301
39DAP/reference	1.16944	0.222
41DAP/reference	1.18253	0.363
42DAP/reference	1.11721	0.233
43DAP/reference	1.21119	0.148
47DAP/reference	0.96331	0.671
52DAP/reference	1.31165	0.021
57DAP/reference	1.12443	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91089	0.318
17DAP/reference	0.95806	0.378
27DAP/reference	1.08601	0.726
39DAP/reference	1.12086	0.705
41DAP/reference	1.019	0.683
42DAP/reference	1.00756	1
43DAP/reference	0.82634	0.033
47DAP/reference	0.87269	0.126
52DAP/reference	0.98132	0.537
57DAP/reference	0.89506	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00062	0.804
17DAP/reference	1.16419	0.203
27DAP/reference	1.25682	0.096
39DAP/reference	1.16793	0.094
41DAP/reference	1.0268	1
42DAP/reference	1.1898	0.307
43DAP/reference	1.10133	0.275
47DAP/reference	0.76844	0.02
52DAP/reference	1.10056	0.79
57DAP/reference	1.24932	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11878	0.966
26DAP/20DAP	1.1145	0.85
34DAP/26DAP	0.82474	0.653
51DAP/34DAP	1.79478	0.775
52DAP/51DAP	1.06051	0.842
53DAP/52DAP	1.5955	0.274
55DAP/53DAP	0.6974	0.293
57DAP/55DAP	0.76488	0.194
62DAP/57DAP	0.93482	0.994
68DAP/62DAP	1.45347	0.034
68DAP/14DAP	1.71159	0.119

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88896	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.83618	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	N/A	N/A
12-4/M82	N/A	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	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	N/A	N/A
7-2/M82	N/A	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	N/A	N/A
IL2-6/WTpooled	0.65666	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04207	1
IL12-4/WTpooled	0.96414	1
IL1-4/WTpooled	0.70407	0.699
WT/WTpooled	0.97269	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	0.66097	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95923	1
DC3000/delta hrp 6h	1.10812	0.95
DC3000/delta hrp 12h	0.97819	1
DC3000/delta hrp 24h	0.70273	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44178	0.074
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	0.98042	1
Exp 36h	0.71726	0.449
Exp 60h	0.62429	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94732	1
Var 0h	1.09452	0.98
Var 12h I row2-row1	0.82471	0.467
Var 12h NI row2-row1	0.97667	0.906
Var 36h I row2-row1	1.13206	1
Var 36h NI row2-row1	1.75807	1
Var 60h I row2-row1	0.92988	0.285
Var 60h NI row2-row1	1.16261	0.904
Time course 0hI-0hNI	0.98654	0.981
Time course 12hI-12hNI	0.93566	0.402
Time course 36hI-36hNI	0.88079	0.095
Time course 60hI-60hNI	0.52124	0.005

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)	1.00575	0.699
transgenic ySAMdc/azygous control (breaker)	1.17345	1
transgenic ySAMdc/azygous control (red)	0.93654	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.78272	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.28465	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.00124	0.093
Manapal/WT (break)	1.34024	0.13
Manapal/WT (red)	1.09873	0.413