Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.6.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.548	0.463
27DAP/17DAP	1.24327	0.749
39DAP/27DAP	1.22537	0.61
41DAP/39DAP	1.24747	0.289
42DAP/41DAP	1.09192	0.92
43DAP/42DAP	1.04796	1
47DAP/43DAP	1.16474	0.842
52DAP/47DAP	1.38073	0.608
57DAP/52DAP	0.90598	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04362	0.735
17DAP/reference	1.05531	0.399
27DAP/reference	1.28631	0.258
39DAP/reference	1.16461	0.197
41DAP/reference	1.0448	0.171
42DAP/reference	1.14147	0.137
43DAP/reference	1.14445	0.024
47DAP/reference	1.17176	0.119
52DAP/reference	1.09749	0.607
57DAP/reference	1.02464	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10875	0.699
27DAP/17DAP	1.21125	0.533
39DAP/27DAP	0.97695	0.844
41DAP/39DAP	1.09465	0.801
42DAP/41DAP	0.90212	0.358
43DAP/42DAP	1.11448	0.478
47DAP/43DAP	1.03119	0.926
52DAP/47DAP	0.8293	0.136
57DAP/52DAP	1.39037	0.276
57DAP/7DAP	1.39557	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08257	0.638
17DAP/reference	0.86832	0.049
27DAP/reference	0.9108	0.117
39DAP/reference	1.24585	0.107
41DAP/reference	1.1112	0.445
42DAP/reference	1.18415	0.308
43DAP/reference	1.16715	0.325
47DAP/reference	1.21976	0.37
52DAP/reference	1.13417	0.491
57DAP/reference	1.06016	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0215	0.933
17DAP/reference	1.07329	0.839
27DAP/reference	1.42231	0.018
39DAP/reference	1.29888	0.082
41DAP/reference	0.9488	0.34
42DAP/reference	1.16869	0.202
43DAP/reference	1.4	0.154
47DAP/reference	1.17904	0.04
52DAP/reference	0.98224	0.537
57DAP/reference	1.03371	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87669	0.268
17DAP/reference	1.10219	0.685
27DAP/reference	0.84296	0.076
39DAP/reference	1.07661	0.691
41DAP/reference	1.17637	0.333
42DAP/reference	1.11234	0.3
43DAP/reference	1.12263	0.241
47DAP/reference	1.04986	0.994
52DAP/reference	0.95799	0.582
57DAP/reference	1.09017	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25219	0.966
26DAP/20DAP	1.15162	0.7
34DAP/26DAP	1.19101	1
51DAP/34DAP	1.50117	0.077
52DAP/51DAP	0.84473	0.151
53DAP/52DAP	1.0062	1
55DAP/53DAP	0.99303	0.876
57DAP/55DAP	3.41521	0.906
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.67253
68DAP/14DAP	0.81213	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14188	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.16312	0.176
Mature Green Tomato/Ripe Tomato	1.48846	0.048
Immature Eggplant/Mature Eggplant	0.91145	0.111
Ripe Pepper/Ripe Tomato	0.49646	0.224
Mature Eggplant/Ripe Tomato	1.04435	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.94496	1
12-2/M82	N/A	N/A
12-4/M82	0.97396	0.619
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	1.12211
4-3-2/M82	0.78784	0.698
4-3/M82	1.11302	1
5-3/M82	1.01797
6-2/M82	N/A	N/A
6-3/M82	0.97857
7-1/M82	1.202
7-2/M82	N/A	N/A
9-3-2/M82	1.06012

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80831	0.247
IL2-6/WTpooled	1.20051	0.46
IL7-5/WTpooled	1.19388
IL7-3/WTpooled	1.15162	1
IL12-4/WTpooled	0.79398	0.566
IL1-4/WTpooled	0.86108	0.834
WT/WTpooled	0.96152	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	1.08436	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08915	0.875
DC3000/delta hrp 6h	0.90575	0.95
DC3000/delta hrp 12h	1.08034	1
DC3000/delta hrp 24h	1.81367	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.70908	0.042
DC3000 delta B/DC3000 delta AB	1.09261	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91421	1
Exp 36h	0.95135	0.879
Exp 60h	0.95442	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03248	1
Var 0h	0.8819	0.933
Var 12h I row2-row1	1.3637	0.211
Var 12h NI row2-row1	0.94413	0.82
Var 36h I row2-row1	0.90429	0.805
Var 36h NI row2-row1	1.06767	0.482
Var 60h I row2-row1	0.82372	0.285
Var 60h NI row2-row1	1.00341	1
Time course 0hI-0hNI	0.96972	0.843
Time course 12hI-12hNI	1.11719	0.216
Time course 36hI-36hNI	1.26934	0.05
Time course 60hI-60hNI	1.81474	0.008

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)	0.92847	0.485
transgenic ySAMdc/azygous control (breaker)	0.81633	0.125
transgenic ySAMdc/azygous control (red)	0.89928	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90299	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62317	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68089	0.172
Manapal/WT (break)	0.96469	1
Manapal/WT (red)	1.20452	0.413