Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07457	0.927
27DAP/17DAP	1.03759	1
39DAP/27DAP	0.66439	0.443
41DAP/39DAP	1.96197	0.416
42DAP/41DAP	1.2924	0.841
43DAP/42DAP	0.94338	0.89
47DAP/43DAP	1.39211	0.659
52DAP/47DAP	1.13291	0.965
57DAP/52DAP	0.96206	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89718	0.109
17DAP/reference	0.96824	0.567
27DAP/reference	0.96525	0.552
39DAP/reference	1.20249	0.129
41DAP/reference	1.17003	0.019
42DAP/reference	1.32486	0.043
43DAP/reference	1.20942	0.008
47DAP/reference	1.28353	0.306
52DAP/reference	1.13542	0.195
57DAP/reference	1.32398	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35714	0.642
27DAP/17DAP	0.76129	0.227
39DAP/27DAP	1.03666	0.845
41DAP/39DAP	0.83169	0.347
42DAP/41DAP	0.92235	0.712
43DAP/42DAP	1.03413	0.664
47DAP/43DAP	0.83076	0.395
52DAP/47DAP	1.36569	0.645
57DAP/52DAP	1.04533	0.926
57DAP/7DAP	1.02303	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86425	0.146
17DAP/reference	0.75946	0.011
27DAP/reference	1.08533	0.16
39DAP/reference	0.89	0.146
41DAP/reference	1.02654	0.977
42DAP/reference	1.06312	0.308
43DAP/reference	1.04931	0.537
47DAP/reference	1.10352	0.254
52DAP/reference	1.34203	0.01
57DAP/reference	1.26387	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96647	0.72
17DAP/reference	1.46816	0.015
27DAP/reference	1.59682	0.014
39DAP/reference	1.46644	0.011
41DAP/reference	1.60018	0.005
42DAP/reference	1.76773	0.008
43DAP/reference	2.93635	0.016
47DAP/reference	1.84591	0.008
52DAP/reference	1.86255	0.008
57DAP/reference	1.45692	0.15

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82438	0.045
17DAP/reference	0.97672	0.624
27DAP/reference	0.93805	0.357
39DAP/reference	1.14965	0.169
41DAP/reference	1.23719	0.486
42DAP/reference	1.10236	0.68
43DAP/reference	0.96016	0.468
47DAP/reference	1.49468	0.006
52DAP/reference	0.94189	0.562
57DAP/reference	2.07095	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85063	0.961
26DAP/20DAP	0.62006
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.82321	0.579
52DAP/51DAP	2.7201
53DAP/52DAP	0.94422	0.848
55DAP/53DAP	1.15613	0.622
57DAP/55DAP	2.15902
62DAP/57DAP	1.37645	0.767
68DAP/62DAP	1.18098	0.253
68DAP/14DAP	1.34631	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.12557	0.496

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.91733
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	4.22076	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94707	0.944
1-1-2/M82	0.96724	1
12-2/M82	N/A	N/A
12-4/M82	1.06562	1
1-3/M82	0.7227	0.33
2-1-1/M82	1.24611	0.457
2-1/M82	N/A	N/A
2-6/M82	0.83299	1
3-2/M82	0.85083
4-1-1/M82	1.08753	1
4-1/M82	1.26771
4-3-2/M82	0.88603	1
4-3/M82	0.80217	0.72
5-3/M82	0.94779	1
6-2/M82	1.05446
6-3/M82	1.00938
7-1/M82	0.84839
7-2/M82	1.14405
9-3-2/M82	0.65369

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99213	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.11868	1
IL12-4/WTpooled	1.09004	0.673
IL1-4/WTpooled	1.08121
WT/WTpooled	1.06511	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99427	1
DC3000/delta hrp 6h	0.97466	0.95
DC3000/delta hrp 12h	1.00558	1
DC3000/delta hrp 24h	0.9826	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90395	0.436
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97313	0.245
Exp 36h	0.66568	0.434
Exp 60h	0.73379	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.16018	0.936
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.04228	0.921
transgenic ySAMdc/azygous control (breaker)	1.02174	1
transgenic ySAMdc/azygous control (red)	1.10703	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98283	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.70114	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.0773	0.381
Manapal/WT (red)	0.73023	0.181