Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.3.19.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85411	0.232
27DAP/17DAP	0.86023	0.631
39DAP/27DAP	1.63813	0.14
41DAP/39DAP	0.98648	0.857
42DAP/41DAP	1.17906	0.877
43DAP/42DAP	1.00639	0.925
47DAP/43DAP	0.83977	0.504
52DAP/47DAP	0.9991	0.927
57DAP/52DAP	1.09066	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5764	0.011
17DAP/reference	0.86271	0.138
27DAP/reference	0.95703	0.471
39DAP/reference	0.96846	0.663
41DAP/reference	0.94317	0.542
42DAP/reference	1.5088	0.001
43DAP/reference	1.0529	0.269
47DAP/reference	1.48362	0.001
52DAP/reference	1.80121	0.008
57DAP/reference	1.53942	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93642	0.509
27DAP/17DAP	0.97155	0.887
39DAP/27DAP	1.16313	0.171
41DAP/39DAP	1.08072	0.801
42DAP/41DAP	0.93313	0.396
43DAP/42DAP	1.18908	0.026
47DAP/43DAP	1.12858	0.3
52DAP/47DAP	0.91043	0.304
57DAP/52DAP	0.98099	0.697
57DAP/7DAP	1.01552	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20572	0.252
17DAP/reference	0.85885	0.011
27DAP/reference	0.81875	0.019
39DAP/reference	0.93644	0.198
41DAP/reference	0.82024	0.086
42DAP/reference	0.67128	0.01
43DAP/reference	0.85899	0.1
47DAP/reference	1.42272	0.44
52DAP/reference	0.7574	0.035
57DAP/reference	0.77491	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25856	0.33
17DAP/reference	1.16972	0.166
27DAP/reference	1.54431	0.143
39DAP/reference	1.42846	0.146
41DAP/reference	1.55115	0.018
42DAP/reference	1.62102	0.008
43DAP/reference	1.01875	0.569
47DAP/reference	1.32606	0.009
52DAP/reference	0.90502	0.187
57DAP/reference	0.90378	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21177	0.026
17DAP/reference	1.02563	0.918
27DAP/reference	0.90697	0.048
39DAP/reference	0.99533	0.755
41DAP/reference	1.00554	0.826
42DAP/reference	1.30424	0.49
43DAP/reference	1.55122	0.209
47DAP/reference	1.2061	0.76
52DAP/reference	1.92066	0.393
57DAP/reference	3.53338	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32424	0.85
26DAP/20DAP	0.98826	1
34DAP/26DAP	0.99552	1
51DAP/34DAP	0.98651	0.873
52DAP/51DAP	1.02161	0.86
53DAP/52DAP	0.99401	0.978
55DAP/53DAP	0.97162	0.775
57DAP/55DAP	1.12408	0.666
62DAP/57DAP	0.87696	0.681
68DAP/62DAP	1.23272	0.664
68DAP/14DAP	1.77466	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20887	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.7955	0.245
Mature Green Tomato/Ripe Tomato	0.3035	0.018
Immature Eggplant/Mature Eggplant	1.46093	0.05
Ripe Pepper/Ripe Tomato	1.14455	1
Mature Eggplant/Ripe Tomato	1.05345	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86666	N/A
1-1-2/M82	1.07307	0.977
12-2/M82	N/A	N/A
12-4/M82	1.32177	1
1-3/M82	1.10957	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	0.66553	0.455
4-1-1/M82	N/A	N/A
4-1/M82	2.4698	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.88465	N/A
6-2/M82	N/A	N/A
6-3/M82	0.70944	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	1.02858	1
IL2-6/WTpooled	1.00102	1
IL7-5/WTpooled	0.76448	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.90621	0.71
IL1-4/WTpooled	0.96497	0.834
WT/WTpooled	0.95946	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	1.0168	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05233	0.921
DC3000/delta hrp 6h	0.96644	0.95
DC3000/delta hrp 12h	1.37004	1
DC3000/delta hrp 24h	1.09566	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0978	0.087
DC3000 delta B/DC3000 delta AB	1.03428	0.593

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88779	1
Exp 36h	1.39947	0.489
Exp 60h	1.37195	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99927	1
Var 0h	0.75618	0.933
Var 12h I row2-row1	1.08228	0.254
Var 12h NI row2-row1	0.9202	0.82
Var 36h I row2-row1	1.17087	0.601
Var 36h NI row2-row1	0.94639	0.645
Var 60h I row2-row1	0.87216	0.306
Var 60h NI row2-row1	1.0844	0.904
Time course 0hI-0hNI	0.9871	0.97
Time course 12hI-12hNI	1.03741	0.572
Time course 36hI-36hNI	1.29539	0.008
Time course 60hI-60hNI	1.51239	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)	1.06319	0.245
transgenic ySAMdc/azygous control (breaker)	1.06257	1
transgenic ySAMdc/azygous control (red)	1.22577	0.92

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	0.77024	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84349	0.172
Manapal/WT (break)	1.33663	0.381
Manapal/WT (red)	1.16474	0.413