Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92131	0.578
27DAP/17DAP	0.81452	0.52
39DAP/27DAP	1.03601	0.798
41DAP/39DAP	0.86503	0.536
42DAP/41DAP	1.51447	0.114
43DAP/42DAP	1.01251	0.937
47DAP/43DAP	1.61484	0.702
52DAP/47DAP	1.09972	0.848
57DAP/52DAP	0.79728	0.708

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80854	0.087
17DAP/reference	0.7692	0.008
27DAP/reference	0.82388	0.036
39DAP/reference	0.81724	0.018
41DAP/reference	0.69344	0.009
42DAP/reference	0.99911	0.531
43DAP/reference	0.86385	0.039
47DAP/reference	1.14326	0.275
52DAP/reference	1.32762	0.149
57DAP/reference	1.25642	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48853	0.189
27DAP/17DAP	1.20116	0.626
39DAP/27DAP	1.20215	0.46
41DAP/39DAP	1.61804	0.868
42DAP/41DAP	0.94937	0.589
43DAP/42DAP	0.83414	0.027
47DAP/43DAP	1.21791	0.127
52DAP/47DAP	0.95807	0.884
57DAP/52DAP	1.00338	0.887
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19061	0.235
17DAP/reference	1.4143	0.01
27DAP/reference	1.19251	0.017
39DAP/reference	1.14358	0.252
41DAP/reference	1.28185	0.159
42DAP/reference	1.37364	0.016
43DAP/reference	1.55415	0.007
47DAP/reference	1.2208	0.136
52DAP/reference	1.46082	0.011
57DAP/reference	1.39866	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74952	0.008
17DAP/reference	0.69935	0.008
27DAP/reference	0.91369	0.16
39DAP/reference	1.05797	1
41DAP/reference	0.98425	0.493
42DAP/reference	0.95705	0.355
43DAP/reference	0.78016	0.072
47DAP/reference	0.81747	0.012
52DAP/reference	0.87952	0.008
57DAP/reference	0.66773	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.119	0.469
17DAP/reference	1.02523	0.87
27DAP/reference	1.4273	0.035
39DAP/reference	1.39435	0.042
41DAP/reference	1.24969	0.096
42DAP/reference	1.27845	0.158
43DAP/reference	1.29905	0.205
47DAP/reference	0.92598	0.191
52DAP/reference	1.09053	0.575
57DAP/reference	1.98546	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02932	1
26DAP/20DAP	1.07118	1
34DAP/26DAP	0.97207	0.998
51DAP/34DAP	0.66392	0.587
52DAP/51DAP	0.88522	1
53DAP/52DAP	1.16336	0.998
55DAP/53DAP	1.02662	0.917
57DAP/55DAP	1.11822	0.947
62DAP/57DAP	0.78521	0.088
68DAP/62DAP	2.35845	0.017
68DAP/14DAP	2.0885	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.45437	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82745	0.282
Mature Green Tomato/Ripe Tomato	1.97767	0.478
Immature Eggplant/Mature Eggplant	1.26291	0.072
Ripe Pepper/Ripe Tomato	1.12211	0.233
Mature Eggplant/Ripe Tomato	0.79278	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80668	0.69
1-1-2/M82	1.16511	1
12-2/M82	0.96079	0.496
12-4/M82	0.85069	1
1-3/M82	1.43015	N/A
2-1-1/M82	0.94361	0.465
2-1/M82	N/A	N/A
2-6/M82	0.91059	N/A
3-2/M82	0.16955	N/A
4-1-1/M82	0.9132	1
4-1/M82	0.52889	0.998
4-3-2/M82	0.87229	1
4-3/M82	1.17272	1
5-3/M82	0.96959	1
6-2/M82	0.8442	1
6-3/M82	0.98682	1
7-1/M82	N/A	N/A
7-2/M82	1.07445	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90463	1
IL2-6/WTpooled	0.99599	1
IL7-5/WTpooled	1.35751	0.75
IL7-3/WTpooled	0.91705	1
IL12-4/WTpooled	1.23446	0.523
IL1-4/WTpooled	0.96365	1
WT/WTpooled	1.12233	0.999

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	1.09286	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97982	1
DC3000/delta hrp 6h	0.90959	0.95
DC3000/delta hrp 12h	1.00013	1
DC3000/delta hrp 24h	1.21647	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26621	N/A
DC3000 delta B/DC3000 delta AB	1.74475	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10018	0.228
Exp 36h	1.0933	1
Exp 60h	1.19808	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05374	N/A
Var 0h	1.12893	0.98
Var 12h I row2-row1	0.8863	0.344
Var 12h NI row2-row1	1.10213	0.649
Var 36h I row2-row1	1.15506	1
Var 36h NI row2-row1	0.76943	0.432
Var 60h I row2-row1	0.84419	0.832
Var 60h NI row2-row1	0.82647	0.756
Time course 0hI-0hNI	0.91878	0.454
Time course 12hI-12hNI	1.07976	0.65
Time course 36hI-36hNI	1.37726	0.017
Time course 60hI-60hNI	3.11794	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)	1.0007	1
transgenic ySAMdc/azygous control (breaker)	1.29587	0.248
transgenic ySAMdc/azygous control (red)	1.06993	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05392	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72302	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90502	1
Manapal/WT (break)	0.74021	0.299
Manapal/WT (red)	0.6018	0.181