Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45988	0.264
27DAP/17DAP	1.29634	0.728
39DAP/27DAP	1.75839	0.063
41DAP/39DAP	0.79533	0.212
42DAP/41DAP	1.22006	0.941
43DAP/42DAP	1.16543	0.991
47DAP/43DAP	1.09476	0.825
52DAP/47DAP	0.57126	0.059
57DAP/52DAP	1.4083	0.589

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88683	0.217
17DAP/reference	1.02165	0.717
27DAP/reference	1.12831	0.071
39DAP/reference	1.07745	0.368
41DAP/reference	0.97802	0.667
42DAP/reference	1.06234	0.093
43DAP/reference	1.18626	0.011
47DAP/reference	1.09664	0.295
52DAP/reference	0.92625	0.073
57DAP/reference	0.97655	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62834	0.093
27DAP/17DAP	0.84251	0.121
39DAP/27DAP	1.45797	0.052
41DAP/39DAP	0.68221	0.093
42DAP/41DAP	1.22513	0.072
43DAP/42DAP	1.76183	0.014
47DAP/43DAP	0.82753	0.102
52DAP/47DAP	1.10902	0.669
57DAP/52DAP	1.03217	0.933
57DAP/7DAP	1.45581	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11824	0.286
17DAP/reference	1.12257	0.199
27DAP/reference	1.00408	0.8
39DAP/reference	1.29416	0.035
41DAP/reference	1.0556	1
42DAP/reference	1.24899	0.03
43DAP/reference	1.35027	0.018
47DAP/reference	1.41844	0.017
52DAP/reference	0.91414	0.278
57DAP/reference	0.89162	0.207

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89476	0.257
17DAP/reference	1.17918	0.034
27DAP/reference	0.99698	0.663
39DAP/reference	0.88144	0.113
41DAP/reference	1.01525	1
42DAP/reference	1.09228	0.233
43DAP/reference	0.93124	0.32
47DAP/reference	0.95365	0.27
52DAP/reference	0.90649	0.121
57DAP/reference	0.89383	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01848	1
17DAP/reference	0.98086	0.647
27DAP/reference	1.02535	0.934
39DAP/reference	1.10293	0.146
41DAP/reference	1.03087	0.84
42DAP/reference	1.13356	0.382
43DAP/reference	1.13966	0.403
47DAP/reference	1.09114	0.48
52DAP/reference	2.21851	0.167
57DAP/reference	1.16243	0.401

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08236	0.966
26DAP/20DAP	0.9625	1
34DAP/26DAP	0.76599	0.682
51DAP/34DAP	1.45504	0.051
52DAP/51DAP	0.71871	0.079
53DAP/52DAP	0.9331	0.807
55DAP/53DAP	1.51432	0.225
57DAP/55DAP	1.24043	0.927
62DAP/57DAP	0.99541	0.994
68DAP/62DAP	0.69981	0.464
68DAP/14DAP	0.60586	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.29891	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55868
Mature Green Tomato/Ripe Tomato	1.22042	0.267
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.43361	0.224
Mature Eggplant/Ripe Tomato	0.0876	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.24547	0.591
1-1-2/M82	0.9277	1
12-2/M82	1.15607	1
12-4/M82	1.52737	1
1-3/M82	1.62215	0.188
2-1-1/M82	1.09015	1
2-1/M82	0.68731	0.325
2-6/M82	1.64105	0.329
3-2/M82	1.38483	0.549
4-1-1/M82	1.58693	0.998
4-1/M82	1.99627	0.853
4-3-2/M82	1.54198	0.246
4-3/M82	1.93064	1
5-3/M82	0.78199	0.642
6-2/M82	1.91263	1
6-3/M82	0.95027	1
7-1/M82	1.01873	0.598
7-2/M82	1.00687	1
9-3-2/M82	2.2633	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.98383	1
IL7-5/WTpooled	1.38317
IL7-3/WTpooled	0.82254	0.298
IL12-4/WTpooled	0.9492	1
IL1-4/WTpooled	1.13543	1
WT/WTpooled	1.00502	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	0.97197	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94218	1
DC3000/delta hrp 6h	0.8772	0.95
DC3000/delta hrp 12h	1.00819	1
DC3000/delta hrp 24h	1.34297	0.059

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	1.25556	1
Exp 36h	N/A	N/A
Exp 60h	0.9942	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1818	1
Var 0h	1.18371	0.936
Var 12h I row2-row1	1.58822	0.296
Var 12h NI row2-row1	1.4751	0.649
Var 36h I row2-row1	1.1319	0.908
Var 36h NI row2-row1	1.09381	1
Var 60h I row2-row1	1.27301	1
Var 60h NI row2-row1	0.88758	0.63
Time course 0hI-0hNI	1.21924	0.227
Time course 12hI-12hNI	0.90732	0.295
Time course 36hI-36hNI	1.19013	0.355
Time course 60hI-60hNI	1.39054	0.009

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)	0.99541	0.931
transgenic ySAMdc/azygous control (breaker)	0.88228	0.49
transgenic ySAMdc/azygous control (red)	0.92027	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99452	0.631

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.39067	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69951	1
Manapal/WT (break)	0.62603	0.333
Manapal/WT (red)	0.81704	0.242