Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93793	0.664
27DAP/17DAP	0.9686	0.947
39DAP/27DAP	0.93306	0.641
41DAP/39DAP	1.02051	1
42DAP/41DAP	0.8393	0.774
43DAP/42DAP	1.3407	0.466
47DAP/43DAP	0.56352	0.071
52DAP/47DAP	1.5175	0.374
57DAP/52DAP	0.81519	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96258	0.254
17DAP/reference	0.92337	0.368
27DAP/reference	1.04354	0.529
39DAP/reference	0.83889	0.035
41DAP/reference	0.74898	0.009
42DAP/reference	1.09213	0.231
43DAP/reference	0.88768	0.211
47DAP/reference	1.01638	1
52DAP/reference	0.9711	0.489
57DAP/reference	0.95817	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87335	0.47
27DAP/17DAP	1.70707
39DAP/27DAP	0.87263	0.572
41DAP/39DAP	1.12067	0.837
42DAP/41DAP	1.06303	1
43DAP/42DAP	1.62939	0.016
47DAP/43DAP	1.10771	0.69
52DAP/47DAP	1.16859	0.593
57DAP/52DAP	1.43957	0.563
57DAP/7DAP	0.48839

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74887	0.025
17DAP/reference	1.28248	0.162
27DAP/reference	1.0908	0.974
39DAP/reference	1.75073	0.032
41DAP/reference	1.21502	0.977
42DAP/reference	2.71604	0.012
43DAP/reference	2.13201	0.014
47DAP/reference	1.33	0.133
52DAP/reference	1.31278	0.098
57DAP/reference	1.60145	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11325	0.582
17DAP/reference	1.0725	0.557
27DAP/reference	0.98176	0.554
39DAP/reference	1.30805	0.119
41DAP/reference	1.28697	0.115
42DAP/reference	0.95279	0.237
43DAP/reference	1.05854	0.809
47DAP/reference	0.83769	0.168
52DAP/reference	1.03432	0.988
57DAP/reference	0.98945	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27615	0.366
17DAP/reference	1.07721	0.865
27DAP/reference	1.5905	0.012
39DAP/reference	1.30795	0.296
41DAP/reference	0.96703	0.618
42DAP/reference	0.9523	0.552
43DAP/reference	1.14396	0.302
47DAP/reference	0.89855	0.199
52DAP/reference	1.35166	0.198
57DAP/reference	1.09276	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11285	0.966
26DAP/20DAP	1.37518	0.19
34DAP/26DAP	0.94896	0.893
51DAP/34DAP	0.89246	0.598
52DAP/51DAP	0.92571	1
53DAP/52DAP	1.25646	0.58
55DAP/53DAP	1.22907	0.689
57DAP/55DAP	0.87837	0.583
62DAP/57DAP	1.307	0.133
68DAP/62DAP	1.40008	0.047
68DAP/14DAP	1.28021	0.036

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49055	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.50729	0.024
Immature Eggplant/Mature Eggplant	1.87631	0.053
Ripe Pepper/Ripe Tomato	0.63418
Mature Eggplant/Ripe Tomato	0.55943	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06789
1-1-2/M82	1.10774	1
12-2/M82	N/A	N/A
12-4/M82	0.6444	0.275
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	N/A	N/A
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	0.70411	0.72
5-3/M82	1.42244	0.572
6-2/M82	4.28642	1
6-3/M82	1.0646	1
7-1/M82	N/A	N/A
7-2/M82	2.60737	0.385
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	0.94275	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.23488	1
IL12-4/WTpooled	0.95227	1
IL1-4/WTpooled	1.126	1
WT/WTpooled	1.02158	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	0.91321	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05841	0.921
DC3000/delta hrp 6h	1.08828	1
DC3000/delta hrp 12h	1.04387	1
DC3000/delta hrp 24h	0.98494	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1092
DC3000 delta B/DC3000 delta AB	1.33344	0.223

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78266	0.265
Exp 36h	0.84776	0.749
Exp 60h	0.8829	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01181
Var 0h	1.16627	1
Var 12h I row2-row1	0.95392	0.856
Var 12h NI row2-row1	1.02535	1
Var 36h I row2-row1	0.99939	1
Var 36h NI row2-row1	0.73467	0.329
Var 60h I row2-row1	0.902	0.285
Var 60h NI row2-row1	0.72416	1
Time course 0hI-0hNI	0.87153	0.069
Time course 12hI-12hNI	1.03022	0.747
Time course 36hI-36hNI	0.87878	0.101
Time course 60hI-60hNI	0.51853	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)	1.03434	0.699
transgenic ySAMdc/azygous control (breaker)	0.97392	1
transgenic ySAMdc/azygous control (red)	0.93991	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0083	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09591	0.307
Manapal/WT (break)	1.07783	0.381
Manapal/WT (red)	1.70663	0.133