Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80169	0.29
27DAP/17DAP	0.89172	0.791
39DAP/27DAP	1.28022	0.593
41DAP/39DAP	0.95228	0.837
42DAP/41DAP	1.168	0.898
43DAP/42DAP	1.0621	1
47DAP/43DAP	1.60523	0.429
52DAP/47DAP	1.21753	0.649
57DAP/52DAP	0.91843	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87539	0.054
17DAP/reference	0.93456	0.18
27DAP/reference	0.96637	0.552
39DAP/reference	0.88862	0.194
41DAP/reference	0.8464	0.009
42DAP/reference	0.92405	0.099
43DAP/reference	0.99396	0.861
47DAP/reference	0.88073	0.042
52DAP/reference	0.84052	0.065
57DAP/reference	1.0134	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.77163	0.719
27DAP/17DAP	1.0621	0.831
39DAP/27DAP	1.16393	0.245
41DAP/39DAP	0.95562	0.91
42DAP/41DAP	1.10907	0.719
43DAP/42DAP	1.04932	0.746
47DAP/43DAP	1.17878	0.406
52DAP/47DAP	0.89671	0.612
57DAP/52DAP	0.96016	0.716
57DAP/7DAP	1.39488	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29286	0.036
17DAP/reference	1.03379	0.688
27DAP/reference	1.10161	0.073
39DAP/reference	1.18363	0.198
41DAP/reference	1.00026	0.778
42DAP/reference	1.01982	0.889
43DAP/reference	1.07356	0.188
47DAP/reference	0.95429	0.504
52DAP/reference	1.15735	0.023
57DAP/reference	1.25974	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15501	0.404
17DAP/reference	1.03306	0.898
27DAP/reference	1.00682	1
39DAP/reference	1.14518	0.128
41DAP/reference	0.87607	0.169
42DAP/reference	0.87333	0.05
43DAP/reference	1.06642	0.769
47DAP/reference	0.80786	0.012
52DAP/reference	0.94601	0.259
57DAP/reference	0.93359	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.53626	0.019
17DAP/reference	1.04024	0.738
27DAP/reference	1.23187	0.059
39DAP/reference	1.13984	0.039
41DAP/reference	1.08933	0.343
42DAP/reference	2.87267	0.032
43DAP/reference	2.09671	0.059
47DAP/reference	0.996	0.646
52DAP/reference	1.24021	0.301
57DAP/reference	1.38663	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07358	0.966
26DAP/20DAP	1.0723	0.941
34DAP/26DAP	1.1156	1
51DAP/34DAP	1.21417	0.483
52DAP/51DAP	1.18254	0.197
53DAP/52DAP	0.68456	0.049
55DAP/53DAP	1.21165	0.834
57DAP/55DAP	1.07478	0.898
62DAP/57DAP	1.16351	0.393
68DAP/62DAP	0.91326	0.668
68DAP/14DAP	1.15506	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89767	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.21668	0.044
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.11144	1
Mature Eggplant/Ripe Tomato	0.57179	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.89875
12-2/M82	N/A	N/A
12-4/M82	1.02986
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	1.14317
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.97711

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86356
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.78512	0.566
IL1-4/WTpooled	1.83755
WT/WTpooled	0.82935

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	1.05156	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97662	1
DC3000/delta hrp 6h	0.84468	0.95
DC3000/delta hrp 12h	0.88854	1
DC3000/delta hrp 24h	0.61206	0.034

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.68253	1
Exp 36h	0.68682	0.623
Exp 60h	0.76239	0.586

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	0.98961	1
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)	1.09388	0.221
transgenic ySAMdc/azygous control (breaker)	0.6676	0.137
transgenic ySAMdc/azygous control (red)	0.95684	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95228	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93993	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63208	0.172
Manapal/WT (break)	0.98085	1
Manapal/WT (red)	0.70138	0.181