Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06223	0.997
27DAP/17DAP	0.94546	0.913
39DAP/27DAP	0.79934	0.414
41DAP/39DAP	0.78431	0.264
42DAP/41DAP	1.00358	1
43DAP/42DAP	0.87201	0.827
47DAP/43DAP	1.23628	0.459
52DAP/47DAP	1.20905	0.67
57DAP/52DAP	0.89945	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87816	0.121
17DAP/reference	0.71471	0.008
27DAP/reference	0.98358	0.694
39DAP/reference	0.92775	0.446
41DAP/reference	0.6329	0.014
42DAP/reference	0.90951	0.015
43DAP/reference	0.96609	0.594
47DAP/reference	1.02363	1
52DAP/reference	1.11236	0.476
57DAP/reference	1.2541	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01523	0.75
27DAP/17DAP	1.23586	0.419
39DAP/27DAP	1.05331	1
41DAP/39DAP	0.89659	0.434
42DAP/41DAP	1.15674	0.935
43DAP/42DAP	1.24503	0.83
47DAP/43DAP	1.12633	0.884
52DAP/47DAP	1.10649	0.649
57DAP/52DAP	1.27028	0.165
57DAP/7DAP	0.92782	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14312	0.65
17DAP/reference	0.68768	0.192
27DAP/reference	1.15017	0.371
39DAP/reference	0.9372	0.411
41DAP/reference	1.03092	0.848
42DAP/reference	0.99988	0.751
43DAP/reference	1.02176	0.665
47DAP/reference	0.94653	0.504
52DAP/reference	1.29787	0.066
57DAP/reference	1.09298	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80382	0.021
17DAP/reference	0.76419	0.01
27DAP/reference	0.9225	0.181
39DAP/reference	1.0025	0.661
41DAP/reference	0.97583	0.422
42DAP/reference	0.9088	0.169
43DAP/reference	0.78703	0.077
47DAP/reference	0.80615	0.017
52DAP/reference	0.9287	0.156
57DAP/reference	0.76519	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40225	0.126
17DAP/reference	1.056	0.9
27DAP/reference	N/A	N/A
39DAP/reference	1.21234	0.563
41DAP/reference	1.08637	1
42DAP/reference	1.18921	0.279
43DAP/reference	1.35244	0.219
47DAP/reference	0.86827	0.114
52DAP/reference	1.43039	0.128
57DAP/reference	1.3071	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02906	1
26DAP/20DAP	1.51269	0.608
34DAP/26DAP	0.83777	0.381
51DAP/34DAP	1.24311	0.073
52DAP/51DAP	0.80167	1
53DAP/52DAP	0.95838	0.811
55DAP/53DAP	0.71152	0.033
57DAP/55DAP	1.21654	0.584
62DAP/57DAP	0.7746	0.681
68DAP/62DAP	1.16682	0.336
68DAP/14DAP	2.03859	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72563	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70067
Mature Green Tomato/Ripe Tomato	0.84447	0.347
Immature Eggplant/Mature Eggplant	0.77719	0.292
Ripe Pepper/Ripe Tomato	1.42125	0.125
Mature Eggplant/Ripe Tomato	1.75722	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.90079
1-3/M82	N/A	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	1.52005
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.22269
6-2/M82	N/A	N/A
6-3/M82	0.80107
7-1/M82	0.93382
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	0.87541	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.35059	0.792
IL7-3/WTpooled	1.88975
IL12-4/WTpooled	1.36295	0.695
IL1-4/WTpooled	0.96168	0.476
WT/WTpooled	0.62532	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	1.12315	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.22022	0.894
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.8949	1
DC3000/delta hrp 24h	0.68183	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16693	0.556
DC3000 delta B/DC3000 delta AB	0.96304	0.729

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	1.04226	1
Var 0h	0.53654	0.936
Var 12h I row2-row1	1.1112	0.654
Var 12h NI row2-row1	1.13133	1
Var 36h I row2-row1	0.95882	1
Var 36h NI row2-row1	0.81612	0.421
Var 60h I row2-row1	0.91795	0.439
Var 60h NI row2-row1	1.02799	1
Time course 0hI-0hNI	0.99086	1
Time course 12hI-12hNI	1.00634	1
Time course 36hI-36hNI	1.03614	0.453
Time course 60hI-60hNI	0.79626	0.007

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)	0.96338	0.454
transgenic ySAMdc/azygous control (breaker)	0.99606	1
transgenic ySAMdc/azygous control (red)	1.1265	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94471	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86098	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17536	0.307
Manapal/WT (break)	0.94661	1
Manapal/WT (red)	1.10794	1