Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86311	0.405
27DAP/17DAP	1.33545	0.804
39DAP/27DAP	1.17742	0.685
41DAP/39DAP	0.7541	0.21
42DAP/41DAP	1.21012	0.825
43DAP/42DAP	0.71874	0.409
47DAP/43DAP	1.00018	0.934
52DAP/47DAP	0.90856	0.675
57DAP/52DAP	1.41503	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98606	0.601
17DAP/reference	0.88941	0.503
27DAP/reference	0.92654	0.134
39DAP/reference	1.24373	0.096
41DAP/reference	1.13209	0.021
42DAP/reference	0.8843	0.233
43DAP/reference	0.8044	0.273
47DAP/reference	1.28271	0.014
52DAP/reference	0.97358	0.489
57DAP/reference	0.55469	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07051	0.482
27DAP/17DAP	0.99086	0.943
39DAP/27DAP	0.78833	0.066
41DAP/39DAP	1.12273	0.469
42DAP/41DAP	1.03664	0.927
43DAP/42DAP	0.75471	0.033
47DAP/43DAP	0.97784	0.902
52DAP/47DAP	0.95802	0.899
57DAP/52DAP	1.12134	0.654
57DAP/7DAP	1.0837

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1656	0.252
17DAP/reference	1.03463	1
27DAP/reference	1.14994	0.06
39DAP/reference	1.0156	1
41DAP/reference	0.94776	0.357
42DAP/reference	1.15907	0.889
43DAP/reference	0.97822	0.502
47DAP/reference	1.14922	0.458
52DAP/reference	0.97387	0.477
57DAP/reference	1.02859	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22893	0.213
17DAP/reference	1.19195	0.278
27DAP/reference	1.16019	0.118
39DAP/reference	1.27497	0.09
41DAP/reference	1.1673	0.513
42DAP/reference	1.14802	0.133
43DAP/reference	1.24039	0.05
47DAP/reference	1.13126	0.256
52DAP/reference	1.06268	0.667
57DAP/reference	1.13895	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22282	0.07
17DAP/reference	1.09633	0.585
27DAP/reference	1.02707	0.805
39DAP/reference	1.13968	0.175
41DAP/reference	1.11595	0.621
42DAP/reference	0.95218	0.552
43DAP/reference	0.96327	0.59
47DAP/reference	1.24612	0.294
52DAP/reference	0.92352	0.472
57DAP/reference	1.37019	0.086

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29656	1
26DAP/20DAP	1.33346	0.22
34DAP/26DAP	0.50392	0.159
51DAP/34DAP	1.06675	0.84
52DAP/51DAP	0.73297	0.151
53DAP/52DAP	0.88266	0.212
55DAP/53DAP	0.96728	0.82
57DAP/55DAP	0.81135	0.601
62DAP/57DAP	0.95652	0.994
68DAP/62DAP	0.80654	0.464
68DAP/14DAP	0.83492	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.54621	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48627
Mature Green Tomato/Ripe Tomato	1.19655	0.363
Immature Eggplant/Mature Eggplant	0.75991	0.077
Ripe Pepper/Ripe Tomato	0.82391	1
Mature Eggplant/Ripe Tomato	1.09614	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06867	0.877
1-1-2/M82	1.07249	1
12-2/M82	0.84846	0.862
12-4/M82	0.6847
1-3/M82	1.48965
2-1-1/M82	0.89727	0.92
2-1/M82	N/A	N/A
2-6/M82	0.85064	1
3-2/M82	N/A	N/A
4-1-1/M82	0.90584	1
4-1/M82	0.86543
4-3-2/M82	N/A	N/A
4-3/M82	0.99386	1
5-3/M82	1.27066	0.572
6-2/M82	0.73509	0.497
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96086
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96252	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.11733	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.00876	1
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	1.08474	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97898	1
DC3000/delta hrp 6h	1.06596	1
DC3000/delta hrp 12h	1.10513	1
DC3000/delta hrp 24h	1.06702	0.728

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	1.00582	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.63423	1
Exp 36h	0.89745	0.82
Exp 60h	0.69576	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00313	1
Var 0h	1.16178	1
Var 12h I row2-row1	0.99944	1
Var 12h NI row2-row1	1.05648	1
Var 36h I row2-row1	1.03223	0.908
Var 36h NI row2-row1	0.43743	0.296
Var 60h I row2-row1	1.20794	0.543
Var 60h NI row2-row1	0.84313	0.313
Time course 0hI-0hNI	0.84183	0.074
Time course 12hI-12hNI	0.95555	0.47
Time course 36hI-36hNI	0.98222	0.54
Time course 60hI-60hNI	0.79901	0.026

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)	1.01561	0.798
transgenic ySAMdc/azygous control (breaker)	1.57751	0.178
transgenic ySAMdc/azygous control (red)	1.07023	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98328	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02793	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32144	0.105
Manapal/WT (break)	1.14069	0.381
Manapal/WT (red)	1.5414	0.133