Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87388	0.551
27DAP/17DAP	0.66658	0.532
39DAP/27DAP	1.22364	0.61
41DAP/39DAP	1.03255	0.946
42DAP/41DAP	2.04924	0.566
43DAP/42DAP	1.19518	0.831
47DAP/43DAP	1.43874	0.187
52DAP/47DAP	1.03215	0.916
57DAP/52DAP	1.12277	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96912	0.526
17DAP/reference	0.91994	0.18
27DAP/reference	1.20699	0.109
39DAP/reference	1.06911	0.639
41DAP/reference	0.96857	0.667
42DAP/reference	1.01926	1
43DAP/reference	1.06053	0.425
47DAP/reference	1.14858	0.023
52DAP/reference	1.21483	0.141
57DAP/reference	1.19914	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44343	0.213
27DAP/17DAP	1.23919	0.9
39DAP/27DAP	0.9567	0.732
41DAP/39DAP	1.18904	0.417
42DAP/41DAP	0.55955	0.01
43DAP/42DAP	1.02156	0.991
47DAP/43DAP	0.9805	0.886
52DAP/47DAP	1.01523	0.913
57DAP/52DAP	0.98493	0.782
57DAP/7DAP	1.91367	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77346	0.1
17DAP/reference	0.81778	0.064
27DAP/reference	0.96937	0.43
39DAP/reference	0.71474	0.064
41DAP/reference	0.58869	0.012
42DAP/reference	0.5191	0.011
43DAP/reference	0.88337	0.21
47DAP/reference	0.90485	0.383
52DAP/reference	0.74906	0.049
57DAP/reference	0.94721	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03028	0.885
17DAP/reference	0.74519	0.035
27DAP/reference	1.00401	0.711
39DAP/reference	1.29232	0.529
41DAP/reference	1.19496	0.642
42DAP/reference	1.00458	0.723
43DAP/reference	1.37146	0.331
47DAP/reference	1.05071	0.639
52DAP/reference	1.02095	0.988
57DAP/reference	0.73243	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78444	0.035
17DAP/reference	1.02007	1
27DAP/reference	0.83205	0.081
39DAP/reference	0.95474	0.464
41DAP/reference	0.85413	0.185
42DAP/reference	1.0425	0.923
43DAP/reference	1.14535	0.688
47DAP/reference	0.9785	0.525
52DAP/reference	1.17508	0.928
57DAP/reference	1.13934	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12544	0.966
26DAP/20DAP	1.18426	0.642
34DAP/26DAP	1.75355	0.819
51DAP/34DAP	1.05042	0.869
52DAP/51DAP	1.1058	0.873
53DAP/52DAP	1.49022	0.196
55DAP/53DAP	0.92625	0.698
57DAP/55DAP	1.31938	0.865
62DAP/57DAP	0.9898	0.994
68DAP/62DAP	1.04352	0.872
68DAP/14DAP	0.9546

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87354	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.4142	0.115
Mature Green Tomato/Ripe Tomato	0.52002	0.2
Immature Eggplant/Mature Eggplant	1.66408
Ripe Pepper/Ripe Tomato	2.20288
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32193	0.432
1-1-2/M82	N/A	N/A
12-2/M82	1.22297
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.08231
2-1/M82	N/A	N/A
2-6/M82	1.19349	1
3-2/M82	0.90134	0.455
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	0.8717	1
6-2/M82	0.91745
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.80275
9-3-2/M82	1.26117

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98676	1
IL2-6/WTpooled	1.11386	0.659
IL7-5/WTpooled	0.75251
IL7-3/WTpooled	1.18637	1
IL12-4/WTpooled	1.01094	0.891
IL1-4/WTpooled	0.90859	0.562
WT/WTpooled	1.06593	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	0.88807	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05552	0.921
DC3000/delta hrp 6h	1.13876	1
DC3000/delta hrp 12h	1.11572	1
DC3000/delta hrp 24h	0.91321	0.346

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.83854
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	1.04042	1
Exp 36h	0.68813	0.504
Exp 60h	0.74971	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02484	1
Var 0h	1.40322	0.421
Var 12h I row2-row1	0.9874	1
Var 12h NI row2-row1	1.13613	0.649
Var 36h I row2-row1	1.01063	0.41
Var 36h NI row2-row1	0.90952	0.432
Var 60h I row2-row1	1.01872	1
Var 60h NI row2-row1	0.87336	0.818
Time course 0hI-0hNI	0.92158	0.418
Time course 12hI-12hNI	0.92724	0.238
Time course 36hI-36hNI	0.83937	0.031
Time course 60hI-60hNI	0.46262	0.006

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)	1.36931	0.253
transgenic ySAMdc/azygous control (breaker)	1.10766	1
transgenic ySAMdc/azygous control (red)	0.96617	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01548	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.65781	0.09
Manapal/WT (break)	1.95403	0.126
Manapal/WT (red)	1.14338	0.413