Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01502	0.964
27DAP/17DAP	1.11985	0.845
39DAP/27DAP	1.02025	1
41DAP/39DAP	1.00415	1
42DAP/41DAP	1.02394	0.983
43DAP/42DAP	0.95503	0.887
47DAP/43DAP	0.99145	0.953
52DAP/47DAP	0.95464	0.842
57DAP/52DAP	1.0048	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94886	0.362
17DAP/reference	0.95586	0.26
27DAP/reference	1.01937	0.759
39DAP/reference	1.03045	0.352
41DAP/reference	0.90685	0.267
42DAP/reference	1.0467	0.311
43DAP/reference	1.00508	0.982
47DAP/reference	1.01	1
52DAP/reference	1.05517	0.695
57DAP/reference	1.06967	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00686	1
27DAP/17DAP	0.99416	0.943
39DAP/27DAP	0.99891	1
41DAP/39DAP	1.00205	1
42DAP/41DAP	1.03054	0.852
43DAP/42DAP	0.99704	1
47DAP/43DAP	1.01345	0.93
52DAP/47DAP	0.93651	0.591
57DAP/52DAP	1.01692	0.911
57DAP/7DAP	0.88385

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56417	0.032
17DAP/reference	2.22156	0.006
27DAP/reference	1.8501	0.007
39DAP/reference	2.11148	0.005
41DAP/reference	2.1592	0.013
42DAP/reference	2.5214	0.006
43DAP/reference	2.70367	0.006
47DAP/reference	1.61919	0.165
52DAP/reference	2.2036	0.007
57DAP/reference	2.00196	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91993	0.14
17DAP/reference	0.94589	0.287
27DAP/reference	0.9513	0.24
39DAP/reference	0.91352	0.034
41DAP/reference	0.94659	0.262
42DAP/reference	1.04874	0.509
43DAP/reference	0.80518	0.084
47DAP/reference	1.00491	1
52DAP/reference	0.94482	0.143
57DAP/reference	0.91505	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48322	0.058
17DAP/reference	1.31099	0.467
27DAP/reference	2.04781	0.031
39DAP/reference	2.36613	0.006
41DAP/reference	1.91687	0.017
42DAP/reference	1.92504	0.013
43DAP/reference	1.87639	0.026
47DAP/reference	0.99166	0.626
52DAP/reference	1.97667	0.115
57DAP/reference	1.58226	0.209

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98874	1
26DAP/20DAP	1.0945	0.647
34DAP/26DAP	1.09635	1
51DAP/34DAP	0.98992	0.901
52DAP/51DAP	1.03677	0.783
53DAP/52DAP	1.01678	1
55DAP/53DAP	1.03201	0.938
57DAP/55DAP	1.09179	0.87
62DAP/57DAP	1.12113
68DAP/62DAP	1.16291	0.17
68DAP/14DAP	1.41086	0.063

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95698	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03989	0.666
Mature Green Tomato/Ripe Tomato	1.00991	0.774
Immature Eggplant/Mature Eggplant	1.26388	0.205
Ripe Pepper/Ripe Tomato	1.37644	1
Mature Eggplant/Ripe Tomato	1.62805	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91572	0.944
1-1-2/M82	1.02138	1
12-2/M82	0.99247	1
12-4/M82	0.95843	0.619
1-3/M82	0.95132	0.501
2-1-1/M82	0.89521	0.465
2-1/M82	0.89662	0.74
2-6/M82	0.96836	1
3-2/M82	0.99962	1
4-1-1/M82	1.0169	1
4-1/M82	1.01836	1
4-3-2/M82	0.80647	0.698
4-3/M82	0.91997	0.72
5-3/M82	0.95634	1
6-2/M82	1.00663	1
6-3/M82	0.99462	1
7-1/M82	0.97558	1
7-2/M82	0.91358	0.599
9-3-2/M82	0.90472	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93695	1
IL2-6/WTpooled	0.79461	0.473
IL7-5/WTpooled	0.77439	1
IL7-3/WTpooled	0.99153	1
IL12-4/WTpooled	1.17411	0.673
IL1-4/WTpooled	0.97031	0.476
WT/WTpooled	1.06355	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	1.50853	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92551
DC3000/delta hrp 6h	1.09929	1
DC3000/delta hrp 12h	0.94358	1
DC3000/delta hrp 24h	1.09409	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34251	0.042
DC3000 delta B/DC3000 delta AB	1.30362	0.162

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01562	1
Exp 36h	0.99429	1
Exp 60h	0.9043	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00846	1
Var 0h	0.86416	1
Var 12h I row2-row1	1.4933	0.272
Var 12h NI row2-row1	1.02492	1
Var 36h I row2-row1	1.10375	1
Var 36h NI row2-row1	0.93465	0.584
Var 60h I row2-row1	0.94581	0.285
Var 60h NI row2-row1	1.16878	1
Time course 0hI-0hNI	1.05876	0.867
Time course 12hI-12hNI	1.06984	0.724
Time course 36hI-36hNI	1.13012	0.028
Time course 60hI-60hNI	2.88219	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)	1.07766	0.339
transgenic ySAMdc/azygous control (breaker)	1.3888	0.248
transgenic ySAMdc/azygous control (red)	1.11696	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98545	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38176	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.27901	0.105
Manapal/WT (break)	1.46099	0.13
Manapal/WT (red)	0.70986	0.184