Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10049	0.786
27DAP/17DAP	1.19006	0.809
39DAP/27DAP	1.26536	0.361
41DAP/39DAP	0.83753	0.506
42DAP/41DAP	1.0431	1
43DAP/42DAP	1.17795	0.823
47DAP/43DAP	1.01192	0.966
52DAP/47DAP	0.90762	0.702
57DAP/52DAP	0.83079	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89585	0.194
17DAP/reference	1.04781	0.384
27DAP/reference	1.04324	0.457
39DAP/reference	1.12761	0.117
41DAP/reference	0.96691	0.667
42DAP/reference	0.89257	0.026
43DAP/reference	1.02445	0.787
47DAP/reference	0.93748	0.191
52DAP/reference	0.97559	0.449
57DAP/reference	1.01058	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08683	0.826
27DAP/17DAP	0.89687	0.821
39DAP/27DAP	1.31393	0.259
41DAP/39DAP	0.91213	0.729
42DAP/41DAP	1.06005	0.947
43DAP/42DAP	1.05425	0.585
47DAP/43DAP	1.03762	0.892
52DAP/47DAP	1.00259	0.941
57DAP/52DAP	0.7722	0.144
57DAP/7DAP	1.09432	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95986	0.183
17DAP/reference	1.06144	0.754
27DAP/reference	0.98508	0.53
39DAP/reference	0.859	0.064
41DAP/reference	0.91425	0.284
42DAP/reference	0.89025	0.13
43DAP/reference	0.93961	0.292
47DAP/reference	0.89783	0.293
52DAP/reference	0.98717	0.571
57DAP/reference	1.0438	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91901	0.457
17DAP/reference	0.91005	0.287
27DAP/reference	0.87798	0.173
39DAP/reference	0.84355	0.044
41DAP/reference	0.85217	0.024
42DAP/reference	0.86013	0.046
43DAP/reference	0.90415	0.147
47DAP/reference	1.01025	0.841
52DAP/reference	0.99578	0.666
57DAP/reference	1.02037	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88157	0.077
17DAP/reference	0.95498	0.508
27DAP/reference	0.95079	0.465
39DAP/reference	0.96834	0.464
41DAP/reference	1.14548	0.205
42DAP/reference	0.95176	0.552
43DAP/reference	1.09319	0.828
47DAP/reference	1.01839	1
52DAP/reference	0.9687	0.747
57DAP/reference	0.85665	0.093

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10572	0.966
26DAP/20DAP	0.73245	0.512
34DAP/26DAP	0.74801	0.472
51DAP/34DAP	1.74841	0.241
52DAP/51DAP	1.6107	0.238
53DAP/52DAP	0.94112	0.776
55DAP/53DAP	1.28941	0.948
57DAP/55DAP	0.91566	0.703
62DAP/57DAP	1.09493	0.935
68DAP/62DAP	1.04168	1
68DAP/14DAP	0.88703	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24282	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.28273	0.69
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.65921	0.224
Mature Eggplant/Ripe Tomato	0.75631	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99057	1
1-1-2/M82	0.94167
12-2/M82	1.00944
12-4/M82	1.0248	1
1-3/M82	0.83585	0.501
2-1-1/M82	1.11869	0.764
2-1/M82	1.52536
2-6/M82	0.99471	1
3-2/M82	N/A	N/A
4-1-1/M82	0.75699
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.08766
5-3/M82	0.89496	0.642
6-2/M82	0.84587	0.481
6-3/M82	1.04096	1
7-1/M82	0.99266
7-2/M82	0.97029	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.76121	0.047

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92485	1
DC3000/delta hrp 6h	0.81192
DC3000/delta hrp 12h	1.12268	1
DC3000/delta hrp 24h	1.21423	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96398
Var 0h	N/A	N/A
Var 12h I row2-row1	1.1826
Var 12h NI row2-row1	1.70916	1
Var 36h I row2-row1	1.43465	0.908
Var 36h NI row2-row1	0.92173	1
Var 60h I row2-row1	1.06559	1
Var 60h NI row2-row1	1.0442	1
Time course 0hI-0hNI	1.01279	1
Time course 12hI-12hNI	0.88386	0.495
Time course 36hI-36hNI	1.114	0.58
Time course 60hI-60hNI	1.15321	0.06

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)	0.97127	0.789
transgenic ySAMdc/azygous control (breaker)	1.42438	0.178
transgenic ySAMdc/azygous control (red)	0.88138	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99931	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16775	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85273	1
Manapal/WT (break)	1.02629	1
Manapal/WT (red)	0.93435	0.607