Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9591	0.752
27DAP/17DAP	0.95367	0.922
39DAP/27DAP	0.88217	0.594
41DAP/39DAP	0.9634	0.833
42DAP/41DAP	1.00047	1
43DAP/42DAP	0.72112	0.534
47DAP/43DAP	1.10763	0.98
52DAP/47DAP	1.18193	0.851
57DAP/52DAP	0.97923	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94917	0.412
17DAP/reference	0.89759	0.278
27DAP/reference	0.96548	0.595
39DAP/reference	0.93499	0.36
41DAP/reference	0.78899	0.201
42DAP/reference	0.94477	0.188
43DAP/reference	0.8801	0.148
47DAP/reference	0.9955	0.445
52DAP/reference	1.09753	0.607
57DAP/reference	1.12969	0.496

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78926	0.096
27DAP/17DAP	0.92911	0.648
39DAP/27DAP	0.91523	0.536
41DAP/39DAP	0.8871	0.713
42DAP/41DAP	0.97605	0.746
43DAP/42DAP	0.94226	0.482
47DAP/43DAP	0.91712	0.63
52DAP/47DAP	0.88338	0.585
57DAP/52DAP	1.12772	0.567
57DAP/7DAP	1.21439	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49901	0.043
17DAP/reference	1.06117	0.297
27DAP/reference	1.49607	0.013
39DAP/reference	2.40812	0.005
41DAP/reference	1.17037	0.26
42DAP/reference	2.06345	0.007
43DAP/reference	2.38474	0.007
47DAP/reference	1.77534	0.155
52DAP/reference	2.10729	0.007
57DAP/reference	1.58993	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1267	0.582
17DAP/reference	1.02943	0.924
27DAP/reference	0.98548	0.663
39DAP/reference	1.25312	0.412
41DAP/reference	0.89006	0.205
42DAP/reference	1.14404	0.634
43DAP/reference	0.94989	0.581
47DAP/reference	0.73608	0.033
52DAP/reference	1.16014	0.208
57DAP/reference	0.75964	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0241	1
17DAP/reference	1.3899	0.163
27DAP/reference	1.91376	0.019
39DAP/reference	2.23028	0.007
41DAP/reference	1.6493	0.008
42DAP/reference	1.61291	0.016
43DAP/reference	1.44227	0.021
47DAP/reference	0.95938	0.478
52DAP/reference	1.36265	0.295
57DAP/reference	1.383	0.053

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.9031	0.058
26DAP/20DAP	0.78073	0.228
34DAP/26DAP	1.34916	0.19
51DAP/34DAP	0.89893	0.428
52DAP/51DAP	1.42723	0.137
53DAP/52DAP	0.92346	0.767
55DAP/53DAP	1.16943	0.722
57DAP/55DAP	0.83009	0.38
62DAP/57DAP	1.04976	N/A
68DAP/62DAP	1.02115	N/A
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77663	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.1974	0.209
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.00556	1
Mature Eggplant/Ripe Tomato	0.12818	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.43271	0.742
1-1-2/M82	1.35599	N/A
12-2/M82	N/A	N/A
12-4/M82	1.15288	0.58
1-3/M82	1.06775	N/A
2-1-1/M82	0.61877	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89815	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.9036	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.84739	N/A
5-3/M82	0.91257	N/A
6-2/M82	N/A	N/A
6-3/M82	0.96957	1
7-1/M82	N/A	N/A
7-2/M82	0.76923	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	0.70501	N/A
IL2-6/WTpooled	1.0065	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98993	N/A
IL12-4/WTpooled	1.12586	0.673
IL1-4/WTpooled	0.86481	0.562
WT/WTpooled	0.99507	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	1.41746	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10104	0.75
DC3000/delta hrp 6h	1.04729	N/A
DC3000/delta hrp 12h	1.04759	1
DC3000/delta hrp 24h	0.87742	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77423	N/A
DC3000 delta B/DC3000 delta AB	0.93065	0.787

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	1.08281	1
Var 0h	0.7444	1
Var 12h I row2-row1	0.87725	0.514
Var 12h NI row2-row1	0.9688	0.906
Var 36h I row2-row1	1.04353	1
Var 36h NI row2-row1	1.04953	0.482
Var 60h I row2-row1	0.96664	0.832
Var 60h NI row2-row1	1.0128	1
Time course 0hI-0hNI	0.85748	1
Time course 12hI-12hNI	1.01082	0.868
Time course 36hI-36hNI	1.03793	0.651
Time course 60hI-60hNI	0.94244	0.161

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)	0.92849	0.485
transgenic ySAMdc/azygous control (breaker)	0.918	0.129
transgenic ySAMdc/azygous control (red)	0.87171	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92086	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97393	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76801	1
Manapal/WT (break)	0.93747	0.333
Manapal/WT (red)	0.85079	0.242