Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75229	0.182
27DAP/17DAP	1.7105	0.761
39DAP/27DAP	1.34353	0.658
41DAP/39DAP	0.71008	0.365
42DAP/41DAP	1.09519	1
43DAP/42DAP	1.33472	0.854
47DAP/43DAP	1.31129	0.42
52DAP/47DAP	1.40193	0.541
57DAP/52DAP	0.94028	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86293	0.246
17DAP/reference	0.95742	0.701
27DAP/reference	0.86446	0.187
39DAP/reference	0.63847	0.035
41DAP/reference	1.21937	0.808
42DAP/reference	0.72583	0.038
43DAP/reference	0.56282
47DAP/reference	0.81118	0.071
52DAP/reference	0.96897	0.564
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84489	0.238
27DAP/17DAP	1.14215	0.598
39DAP/27DAP	1.04299	0.758
41DAP/39DAP	1.55296	0.276
42DAP/41DAP	0.85182	0.224
43DAP/42DAP	1.1074	0.513
47DAP/43DAP	0.88212	0.577
52DAP/47DAP	1.10642	0.645
57DAP/52DAP	0.99489	0.828
57DAP/7DAP	1.13669	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01233	0.758
17DAP/reference	1.08772	0.147
27DAP/reference	1.16108	0.246
39DAP/reference	1.58144	0.008
41DAP/reference	1.22194	0.336
42DAP/reference	1.5101	0.016
43DAP/reference	1.61152	0.02
47DAP/reference	1.24716	0.075
52DAP/reference	1.43446	0.024
57DAP/reference	2.26495	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94181	0.532
17DAP/reference	0.87836	0.116
27DAP/reference	0.89186	0.292
39DAP/reference	0.85873	0.047
41DAP/reference	0.84755	0.188
42DAP/reference	0.90306	0.169
43DAP/reference	1.68494	0.284
47DAP/reference	1.03699	0.658
52DAP/reference	0.7476	0.007
57DAP/reference	0.74741	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90925	0.197
17DAP/reference	1.06407	0.488
27DAP/reference	0.89592	0.174
39DAP/reference	1.07782	1
41DAP/reference	1.03611	0.826
42DAP/reference	1.06843	1
43DAP/reference	0.9339	0.432
47DAP/reference	0.91924	0.259
52DAP/reference	1.06022	0.928
57DAP/reference	0.90863	0.158

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99802	1
26DAP/20DAP	0.84467	0.512
34DAP/26DAP	1.01765	1
51DAP/34DAP	1.02201	1
52DAP/51DAP	1.23764	0.171
53DAP/52DAP	1.14721	0.23
55DAP/53DAP	1.0124	0.951
57DAP/55DAP	1.13224	0.626
62DAP/57DAP	1.20231	0.8
68DAP/62DAP	1.07043	0.931
68DAP/14DAP	1.18968	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68488	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.17463	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.32773	0.224
Mature Eggplant/Ripe Tomato	0.18065	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.94435
12-2/M82	0.71147
12-4/M82	0.95046	1
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	1.38485
5-3/M82	0.94161	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.79153
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	0.48469	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.33192
IL12-4/WTpooled	0.46465	0.581
IL1-4/WTpooled	1.13899	1
WT/WTpooled	1.28664	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	1.29426	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06128	0.921
DC3000/delta hrp 6h	0.8143	0.95
DC3000/delta hrp 12h	1.1805	1
DC3000/delta hrp 24h	0.85724	0.117

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85464
DC3000 delta B/DC3000 delta AB	1.00849	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17768	1
Exp 36h	0.84254	0.661
Exp 60h	0.94614	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89925	1
Var 0h	1.13922	0.98
Var 12h I row2-row1	1.0335	0.736
Var 12h NI row2-row1	0.98021	0.906
Var 36h I row2-row1	1.03506	1
Var 36h NI row2-row1	0.98061	0.743
Var 60h I row2-row1	0.76692
Var 60h NI row2-row1	0.92329	0.69
Time course 0hI-0hNI	1.06385	0.867
Time course 12hI-12hNI	1.04169	0.785
Time course 36hI-36hNI	1.03371	0.89
Time course 60hI-60hNI	1.46037	0.033

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)	1.01652	0.921
transgenic ySAMdc/azygous control (breaker)	1.07004	1
transgenic ySAMdc/azygous control (red)	0.94936	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0389	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60565	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02068	1
Manapal/WT (break)	1.20622	1
Manapal/WT (red)	1.09411	1