Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42373	0.224
27DAP/17DAP	0.74234	0.287
39DAP/27DAP	0.84893	0.537
41DAP/39DAP	0.82422	0.315
42DAP/41DAP	0.8742	1
43DAP/42DAP	0.87689	0.7
47DAP/43DAP	0.82957	0.484
52DAP/47DAP	1.56155	0.538
57DAP/52DAP	1.0145	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65747	0.041
17DAP/reference	0.50296	0.007
27DAP/reference	0.60711	0.013
39DAP/reference	0.62623	0.021
41DAP/reference	0.50058	0.009
42DAP/reference	0.60452	0.001
43DAP/reference	0.42738	0.013
47DAP/reference	0.61371	0.001
52DAP/reference	0.70275	0.049
57DAP/reference	0.77482	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65193	0.036
27DAP/17DAP	0.7569	0.206
39DAP/27DAP	0.59535	0.029
41DAP/39DAP	1.24134	0.124
42DAP/41DAP	0.91631	0.399
43DAP/42DAP	0.72886	0.023
47DAP/43DAP	0.99472	0.983
52DAP/47DAP	0.94651	0.839
57DAP/52DAP	0.91448	0.476
57DAP/7DAP	0.87427	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89027	0.115
17DAP/reference	0.65195	0.012
27DAP/reference	0.82715	0.117
39DAP/reference	0.44353	0.011
41DAP/reference	0.44797	0.011
42DAP/reference	0.46922	0.01
43DAP/reference	0.26957	0.008
47DAP/reference	0.47814	0.04
52DAP/reference	0.29973	0.009
57DAP/reference	0.30643	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45488	0.007
17DAP/reference	0.57653	0.023
27DAP/reference	0.80658	0.181
39DAP/reference	0.66941	0.056
41DAP/reference	0.68742	0.036
42DAP/reference	0.78584	0.05
43DAP/reference	0.50326	0.004
47DAP/reference	0.80092	0.053
52DAP/reference	0.44357	0.003
57DAP/reference	0.40474	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35763	0.019
17DAP/reference	1.69003	0.109
27DAP/reference	1.04161	0.883
39DAP/reference	0.83886	0.076
41DAP/reference	0.76195	0.086
42DAP/reference	0.7581	0.108
43DAP/reference	0.68735	0.066
47DAP/reference	0.56881	0.006
52DAP/reference	0.5009	0.059
57DAP/reference	1.62439	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87438	0.915
26DAP/20DAP	1.03808	1
34DAP/26DAP	0.9305	0.857
51DAP/34DAP	0.62578	0.083
52DAP/51DAP	0.95081	1
53DAP/52DAP	0.67961	0.049
55DAP/53DAP	0.89486	0.154
57DAP/55DAP	0.86732	0.506
62DAP/57DAP	1.15042	0.098
68DAP/62DAP	1.07158	0.89
68DAP/14DAP	1.31744	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6236	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.23603	0.058
Mature Green Tomato/Ripe Tomato	1.85025	0.018
Immature Eggplant/Mature Eggplant	0.4132	0.062
Ripe Pepper/Ripe Tomato	24.3211	0.256
Mature Eggplant/Ripe Tomato	21.5184	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21285	0.877
1-1-2/M82	0.77251
12-2/M82	1.42109	0.519
12-4/M82	1.21795
1-3/M82	1.05356
2-1-1/M82	0.77654
2-1/M82	N/A	N/A
2-6/M82	0.82595	1
3-2/M82	0.84469
4-1-1/M82	0.97664	1
4-1/M82	N/A	N/A
4-3-2/M82	0.82495
4-3/M82	0.91832	0.611
5-3/M82	1.0621	1
6-2/M82	N/A	N/A
6-3/M82	0.65569
7-1/M82	N/A	N/A
7-2/M82	0.61403
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.00131	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00065	1
DC3000/delta hrp 6h	1.00423	1
DC3000/delta hrp 12h	0.94158	1
DC3000/delta hrp 24h	0.99523	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42613	0.024
DC3000 delta B/DC3000 delta AB	0.36713	0.02

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	0.90211	1
Var 0h	1.35354	0.98
Var 12h I row2-row1	0.76732	0.39
Var 12h NI row2-row1	0.95948	0.713
Var 36h I row2-row1	0.88213	0.805
Var 36h NI row2-row1	1.09433	1
Var 60h I row2-row1	1.55749	0.562
Var 60h NI row2-row1	1.11405	0.904
Time course 0hI-0hNI	1.04682	0.852
Time course 12hI-12hNI	0.98056	0.897
Time course 36hI-36hNI	0.82438	0.04
Time course 60hI-60hNI	0.14926	0.006

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)	0.85958	0.485
transgenic ySAMdc/azygous control (breaker)	2.81835	0.162
transgenic ySAMdc/azygous control (red)	0.97713	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7036	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.01849	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	26.5161	0.083
Manapal/WT (break)	8.14964	0.126
Manapal/WT (red)	2.81916	1