Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88081	0.551
27DAP/17DAP	1.0501	0.902
39DAP/27DAP	0.79727	0.447
41DAP/39DAP	1.48816	0.408
42DAP/41DAP	1.03119	1
43DAP/42DAP	0.87238	0.572
47DAP/43DAP	0.88625	0.645
52DAP/47DAP	1.11969	0.773
57DAP/52DAP	1.08254	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01214	1
17DAP/reference	0.98649	0.701
27DAP/reference	0.95335	0.257
39DAP/reference	0.96392	0.446
41DAP/reference	0.96197	0.341
42DAP/reference	0.98526	0.372
43DAP/reference	0.98651	0.675
47DAP/reference	0.93009	0.032
52DAP/reference	0.91388	0.143
57DAP/reference	0.83281	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96573	0.56
27DAP/17DAP	1.01859	0.954
39DAP/27DAP	1.00034	1
41DAP/39DAP	0.97154	0.934
42DAP/41DAP	1.00462	1
43DAP/42DAP	1.03716	0.413
47DAP/43DAP	0.98271	0.911
52DAP/47DAP	1.03082	0.868
57DAP/52DAP	0.99932	0.913
57DAP/7DAP	1.08277	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96804	0.07
17DAP/reference	0.97175	0.094
27DAP/reference	0.95993	0.076
39DAP/reference	0.99366	0.552
41DAP/reference	0.92281	0.019
42DAP/reference	0.92111	0.013
43DAP/reference	0.98984	0.48
47DAP/reference	0.88033	0.079
52DAP/reference	0.94536	0.106
57DAP/reference	0.94344	0.059

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0826	0.261
17DAP/reference	1.0633	0.278
27DAP/reference	0.99819	0.735
39DAP/reference	1.0216	0.978
41DAP/reference	0.93061	0.152
42DAP/reference	0.89786	0.012
43DAP/reference	1.02025	0.977
47DAP/reference	0.88532	0.016
52DAP/reference	1.05355	0.114
57DAP/reference	1.0592	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01548	0.939
17DAP/reference	0.99376	0.792
27DAP/reference	0.96716	0.184
39DAP/reference	0.97448	0.246
41DAP/reference	0.90819	0.037
42DAP/reference	0.95992	0.134
43DAP/reference	0.9195	0.197
47DAP/reference	0.88076	0.076
52DAP/reference	0.9414	0.464
57DAP/reference	0.7224	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99855	1
26DAP/20DAP	1.01173	1
34DAP/26DAP	0.96249	0.834
51DAP/34DAP	1.01991	0.854
52DAP/51DAP	1.09446	0.323
53DAP/52DAP	0.94967	0.891
55DAP/53DAP	0.76032	N/A
57DAP/55DAP	0.95978	0.839
62DAP/57DAP	1.13007	0.133
68DAP/62DAP	0.96224	0.81
68DAP/14DAP	1.06374	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82148	0.076

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6379	0.21
Mature Green Tomato/Ripe Tomato	1.04756	0.948
Immature Eggplant/Mature Eggplant	0.68454	N/A
Ripe Pepper/Ripe Tomato	1.55594	1
Mature Eggplant/Ripe Tomato	1.11333	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94642	0.708
1-1-2/M82	1.06555	N/A
12-2/M82	1.02164	1
12-4/M82	1.02257	1
1-3/M82	0.87284	N/A
2-1-1/M82	1.20672	0.284
2-1/M82	N/A	N/A
2-6/M82	0.97944	1
3-2/M82	1.02161	N/A
4-1-1/M82	0.71196	N/A
4-1/M82	0.87742	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.81909	1
5-3/M82	1.01893	1
6-2/M82	1.03951	1
6-3/M82	0.92983	1
7-1/M82	N/A	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	1.12518	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.86273	N/A
IL1-4/WTpooled	N/A	N/A
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	1.07755	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08114	0.692
DC3000/delta hrp 6h	0.84049	0.95
DC3000/delta hrp 12h	1.07607	1
DC3000/delta hrp 24h	1.11773	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83546	0.513
DC3000 delta B/DC3000 delta AB	1.03157	0.609

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.74433	0.393
Exp 60h	0.90186	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96269	1
Var 0h	1.34206	0.311
Var 12h I row2-row1	1.10755	0.189
Var 12h NI row2-row1	0.9118	0.82
Var 36h I row2-row1	0.98464	1
Var 36h NI row2-row1	0.83299	0.45
Var 60h I row2-row1	1.1486	0.562
Var 60h NI row2-row1	1.12129	0.904
Time course 0hI-0hNI	1.05723	0.852
Time course 12hI-12hNI	1.03167	0.82
Time course 36hI-36hNI	1.06144	0.19
Time course 60hI-60hNI	1.28185	0.012

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)	1.00989	0.863
transgenic ySAMdc/azygous control (breaker)	1.0139	1
transgenic ySAMdc/azygous control (red)	1.28952	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00727	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16383	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.648	0.09
Manapal/WT (break)	1.53523	0.381
Manapal/WT (red)	1.30387	0.164