Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.2.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8053	0.095
27DAP/17DAP	0.96605	0.964
39DAP/27DAP	1.15784	0.685
41DAP/39DAP	0.9557	0.815
42DAP/41DAP	1.19586	0.671
43DAP/42DAP	0.73294	0.454
47DAP/43DAP	1.2543	0.208
52DAP/47DAP	0.95129	0.786
57DAP/52DAP	1.23193	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15514	0.147
17DAP/reference	1.09705	0.201
27DAP/reference	0.97109	0.642
39DAP/reference	1.10208	0.413
41DAP/reference	0.95237	0.667
42DAP/reference	1.00925	1
43DAP/reference	0.75506	0.118
47DAP/reference	0.83673	0.023
52DAP/reference	0.79352	0.058
57DAP/reference	5.39859	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11871	0.208
27DAP/17DAP	0.99837	0.969
39DAP/27DAP	0.88618	0.156
41DAP/39DAP	0.98533	0.986
42DAP/41DAP	0.98309	0.784
43DAP/42DAP	1.38902	0.016
47DAP/43DAP	0.98731	0.939
52DAP/47DAP	0.8381	0.255
57DAP/52DAP	0.69311	0.099
57DAP/7DAP	0.86266	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29451	0.029
17DAP/reference	1.05069	1
27DAP/reference	1.05729	0.974
39DAP/reference	1.03902	0.745
41DAP/reference	1.0404	1
42DAP/reference	1.111	0.534
43DAP/reference	0.94644	0.385
47DAP/reference	0.97113	0.504
52DAP/reference	0.8872	0.213
57DAP/reference	1.01336	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26908	0.249
17DAP/reference	1.32268	0.037
27DAP/reference	1.11706	0.163
39DAP/reference	1.1278	0.136
41DAP/reference	1.03894	1
42DAP/reference	0.95174	0.355
43DAP/reference	1.12125	0.827
47DAP/reference	0.94132	0.227
52DAP/reference	1.05048	0.528
57DAP/reference	0.89153	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20327	0.122
17DAP/reference	0.98116	0.668
27DAP/reference	0.9866	0.691
39DAP/reference	0.86366	0.111
41DAP/reference	0.93344	0.417
42DAP/reference	0.85478	0.087
43DAP/reference	0.92997	0.348
47DAP/reference	0.93774	0.286
52DAP/reference	0.90792	0.464
57DAP/reference	0.83928	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12217	0.966
26DAP/20DAP	1.34191	0.131
34DAP/26DAP	1.18762	0.819
51DAP/34DAP	0.73714	0.06
52DAP/51DAP	0.79055	0.151
53DAP/52DAP	1.16868	0.608
55DAP/53DAP	0.86584	0.273
57DAP/55DAP	0.92611	0.691
62DAP/57DAP	1.07692	0.935
68DAP/62DAP	0.92939	0.787
68DAP/14DAP	0.73712	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.40621	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61852	0.175
Mature Green Tomato/Ripe Tomato	1.21385	0.267
Immature Eggplant/Mature Eggplant	1.08049	0.215
Ripe Pepper/Ripe Tomato	1.23049	1
Mature Eggplant/Ripe Tomato	1.7314	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08296	1
1-1-2/M82	0.92053	N/A
12-2/M82	1.06185	1
12-4/M82	0.80501	0.298
1-3/M82	0.99698	N/A
2-1-1/M82	1.19759	N/A
2-1/M82	N/A	N/A
2-6/M82	1.02084	0.594
3-2/M82	1.02861	N/A
4-1-1/M82	0.99674	1
4-1/M82	0.90712	N/A
4-3-2/M82	1.40492	N/A
4-3/M82	1.27949	1
5-3/M82	1.19872	0.572
6-2/M82	N/A	N/A
6-3/M82	0.79227	0.68
7-1/M82	1.09286	1
7-2/M82	0.88022	0.57
9-3-2/M82	1.28185	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78735	N/A
IL2-6/WTpooled	1.24323	N/A
IL7-5/WTpooled	0.83306	1
IL7-3/WTpooled	0.87436	0.418
IL12-4/WTpooled	1.3281	0.646
IL1-4/WTpooled	0.81446	0.415
WT/WTpooled	1.10694	0.911

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	1.25237	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07763	0.914
DC3000/delta hrp 6h	0.92705	0.95
DC3000/delta hrp 12h	1.02493	1
DC3000/delta hrp 24h	1.22059	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23438	0.087
DC3000 delta B/DC3000 delta AB	1.25223	0.119

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97996	1
Exp 36h	1.31525	0.693
Exp 60h	1.32232	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02003	1
Var 0h	1.03524	0.98
Var 12h I row2-row1	0.95958	0.856
Var 12h NI row2-row1	0.96198	0.906
Var 36h I row2-row1	0.99241	1
Var 36h NI row2-row1	1.17662	1
Var 60h I row2-row1	2.03296	1
Var 60h NI row2-row1	1.03435	0.904
Time course 0hI-0hNI	1.00891	1
Time course 12hI-12hNI	1.03587	0.81
Time course 36hI-36hNI	0.89578	0.153
Time course 60hI-60hNI	0.60173	0.007

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)	0.9316	0.428
transgenic ySAMdc/azygous control (breaker)	0.81297	0.15
transgenic ySAMdc/azygous control (red)	1.05277	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01098	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81476	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04354	1
Manapal/WT (break)	0.99737	1
Manapal/WT (red)	1.20979	0.413