Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.8.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82868	0.436
27DAP/17DAP	1.07235	0.926
39DAP/27DAP	0.85911	0.482
41DAP/39DAP	0.82166	0.396
42DAP/41DAP	1.9799	0.361
43DAP/42DAP	1.11315	0.993
47DAP/43DAP	1.82945	0.208
52DAP/47DAP	0.9385	0.8
57DAP/52DAP	0.86876	0.768

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73503	0.024
17DAP/reference	0.84052	0.024
27DAP/reference	0.96795	0.595
39DAP/reference	1.13701	0.628
41DAP/reference	0.8752	0.114
42DAP/reference	0.85784	0.046
43DAP/reference	1.25309	0.047
47DAP/reference	1.45851	0.001
52DAP/reference	1.29694	0.018
57DAP/reference	1.02592	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19709	0.605
27DAP/17DAP	1.04504	0.919
39DAP/27DAP	1.13894	0.575
41DAP/39DAP	0.80914	0.265
42DAP/41DAP	1.23626	0.155
43DAP/42DAP	1.85474	0.019
47DAP/43DAP	0.98238	0.919
52DAP/47DAP	0.98623	0.93
57DAP/52DAP	1.12897	0.58
57DAP/7DAP	1.37166	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99585	0.682
17DAP/reference	0.86146	0.108
27DAP/reference	0.93219	N/A
39DAP/reference	1.13778	0.411
41DAP/reference	0.8491	0.139
42DAP/reference	0.97311	0.506
43DAP/reference	1.35217	0.457
47DAP/reference	0.99236	0.671
52DAP/reference	1.03967	1
57DAP/reference	1.13295	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87552	0.238
17DAP/reference	0.91978	0.182
27DAP/reference	0.93216	0.366
39DAP/reference	0.88112	0.214
41DAP/reference	0.83792	0.173
42DAP/reference	0.85719	0.073
43DAP/reference	0.8271	0.114
47DAP/reference	0.92545	0.277
52DAP/reference	0.81646	0.086
57DAP/reference	1.01384	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76457	0.065
17DAP/reference	0.84244	0.167
27DAP/reference	0.98029	0.763
39DAP/reference	0.7014	0.199
41DAP/reference	1.06788	0.984
42DAP/reference	1.42922	0.612
43DAP/reference	1.20185	0.229
47DAP/reference	1.34582	0.007
52DAP/reference	1.66113	0.082
57DAP/reference	1.07706	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.51517	0.752
26DAP/20DAP	0.95734	1
34DAP/26DAP	1.14971	0.819
51DAP/34DAP	1.06801	0.909
52DAP/51DAP	1.02298	1
53DAP/52DAP	1.34523	0.783
55DAP/53DAP	0.9307	0.735
57DAP/55DAP	0.887	0.688
62DAP/57DAP	1.11932	0.622
68DAP/62DAP	0.89385	0.834
68DAP/14DAP	1.32177	0.161

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.00513	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.56632	0.197
Mature Green Tomato/Ripe Tomato	0.1416	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.54713	0.224
Mature Eggplant/Ripe Tomato	0.11711	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18016	0.877
1-1-2/M82	1.07674	1
12-2/M82	0.92199	0.955
12-4/M82	1.07512	1
1-3/M82	N/A	N/A
2-1-1/M82	0.86274	0.465
2-1/M82	0.34583	N/A
2-6/M82	N/A	N/A
3-2/M82	1.36643	0.967
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.04569	N/A
4-3/M82	1.24391	1
5-3/M82	0.95444	1
6-2/M82	N/A	N/A
6-3/M82	0.81936	1
7-1/M82	1.19312	N/A
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	1.05787	1
IL2-6/WTpooled	1.23874	0.46
IL7-5/WTpooled	0.62961	1
IL7-3/WTpooled	1.06168	1
IL12-4/WTpooled	0.81817	0.581
IL1-4/WTpooled	1.08689	1
WT/WTpooled	0.84255	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	0.87841	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0755	0.921
DC3000/delta hrp 6h	0.91581	0.95
DC3000/delta hrp 12h	1.44433	1
DC3000/delta hrp 24h	1.09317	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.49392	0.029
DC3000 delta B/DC3000 delta AB	0.44828	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12155	1
Exp 36h	1.75634	0.409
Exp 60h	1.69408	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04429	1
Var 0h	1.193	1
Var 12h I row2-row1	0.88352	0.705
Var 12h NI row2-row1	0.99695	1
Var 36h I row2-row1	0.87393	0.805
Var 36h NI row2-row1	1.08138	1
Var 60h I row2-row1	1.13653	1
Var 60h NI row2-row1	1.09849	0.904
Time course 0hI-0hNI	1.09209	0.603
Time course 12hI-12hNI	0.93856	0.26
Time course 36hI-36hNI	0.92592	0.255
Time course 60hI-60hNI	0.4464	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)	1.15149	0.482
transgenic ySAMdc/azygous control (breaker)	0.85228	0.49
transgenic ySAMdc/azygous control (red)	0.98148	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08314	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.3952	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32946	0.307
Manapal/WT (break)	1.34254	0.381
Manapal/WT (red)	1.53945	0.222