Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98074	0.752
27DAP/17DAP	1.30666	0.92
39DAP/27DAP	1.1044	0.84
41DAP/39DAP	1.59657	0.37
42DAP/41DAP	1.48909	0.876
43DAP/42DAP	1.02834	0.937
47DAP/43DAP	1.13525	1
52DAP/47DAP	1.3695	0.639
57DAP/52DAP	1.08542	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9129	0.159
17DAP/reference	1.0383	0.127
27DAP/reference	0.99373	0.797
39DAP/reference	1.08546	0.02
41DAP/reference	1.01192	1
42DAP/reference	0.90731	0.023
43DAP/reference	1.05883	0.269
47DAP/reference	0.87263	0.013
52DAP/reference	0.89809	0.172
57DAP/reference	0.99408	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01052	1
27DAP/17DAP	1.04709	0.942
39DAP/27DAP	1.07383	0.626
41DAP/39DAP	0.9154	0.68
42DAP/41DAP	1.0732	0.727
43DAP/42DAP	1.07087	0.513
47DAP/43DAP	0.96951	0.87
52DAP/47DAP	0.94285	0.824
57DAP/52DAP	0.9327	0.334
57DAP/7DAP	1.02802	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94443	0.296
17DAP/reference	0.92077	0.021
27DAP/reference	1.01099	0.974
39DAP/reference	0.91537	0.014
41DAP/reference	0.86483	0.014
42DAP/reference	0.87947	0.01
43DAP/reference	0.86332	0.082
47DAP/reference	0.98137	0.671
52DAP/reference	0.84415	0.04
57DAP/reference	0.83932	0.025

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99816	0.907
17DAP/reference	0.93513	0.214
27DAP/reference	0.94609	0.381
39DAP/reference	0.89031	0.045
41DAP/reference	0.90614	0.177
42DAP/reference	0.97851	0.534
43DAP/reference	1.15811	0.144
47DAP/reference	1.07226	0.321
52DAP/reference	0.99729	0.713
57DAP/reference	1.08284	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95085	0.169
17DAP/reference	1.00941	0.988
27DAP/reference	0.9255	0.195
39DAP/reference	0.92884	0.133
41DAP/reference	0.9523	0.237
42DAP/reference	0.95567	0.361
43DAP/reference	0.90117	0.188
47DAP/reference	0.976	0.525
52DAP/reference	1.01335	0.99
57DAP/reference	0.90785	0.283

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9952	1
26DAP/20DAP	0.83782	1
34DAP/26DAP	0.98407	0.954
51DAP/34DAP	0.9503	0.758
52DAP/51DAP	1.34457	0.035
53DAP/52DAP	0.95705	0.848
55DAP/53DAP	0.97172	0.807
57DAP/55DAP	1.13698	0.694
62DAP/57DAP	1.06046	0.935
68DAP/62DAP	1.0649	1
68DAP/14DAP	1.03112	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.66352	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.86968
Immature Eggplant/Mature Eggplant	0.9149
Ripe Pepper/Ripe Tomato	0.8822	1
Mature Eggplant/Ripe Tomato	0.80505	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10922	0.742
1-1-2/M82	0.84728	0.958
12-2/M82	1.01974	0.296
12-4/M82	0.90275	1
1-3/M82	0.93275	1
2-1-1/M82	1.21747
2-1/M82	1.22718	1
2-6/M82	0.97361	1
3-2/M82	0.91996	1
4-1-1/M82	1.05072	1
4-1/M82	0.72227	0.737
4-3-2/M82	0.87413	1
4-3/M82	0.67645	0.374
5-3/M82	0.9819	1
6-2/M82	0.87622
6-3/M82	0.98748	1
7-1/M82	0.85255
7-2/M82	0.90312	0.881
9-3-2/M82	0.98572	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72134	0.321
IL2-6/WTpooled	1.13094	0.441
IL7-5/WTpooled	0.803	1
IL7-3/WTpooled	1.0693	1
IL12-4/WTpooled	0.79796	1
IL1-4/WTpooled	1.69702	1
WT/WTpooled	0.83669	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	1.24168	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97878	1
DC3000/delta hrp 6h	0.94596	0.95
DC3000/delta hrp 12h	1.17104	1
DC3000/delta hrp 24h	1.16369	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26556	0.229
DC3000 delta B/DC3000 delta AB	1.09029	0.449

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15521	1
Exp 36h	N/A	N/A
Exp 60h	1.38623	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97009	1
Var 0h	0.96145	0.933
Var 12h I row2-row1	1.08517	0.204
Var 12h NI row2-row1	0.8888	0.627
Var 36h I row2-row1	1.04357	1
Var 36h NI row2-row1	0.99672	1
Var 60h I row2-row1	1.02504	1
Var 60h NI row2-row1	1.26738	0.904
Time course 0hI-0hNI	1.07807	0.799
Time course 12hI-12hNI	1.00565	1
Time course 36hI-36hNI	1.0508	0.651
Time course 60hI-60hNI	1.62385	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)	1.0118	0.798
transgenic ySAMdc/azygous control (breaker)	1.35525	0.178
transgenic ySAMdc/azygous control (red)	1.04182	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05269	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92097	0.308

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)	0.89175	1
Manapal/WT (red)	1.15005	0.413