Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.1.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10443	0.812
27DAP/17DAP	1.4951	0.761
39DAP/27DAP	1.39458	0.553
41DAP/39DAP	1.21867	0.392
42DAP/41DAP	0.96056	1
43DAP/42DAP	1.06749	1
47DAP/43DAP	0.93293	0.746
52DAP/47DAP	1.10701	0.902
57DAP/52DAP	1.51044	0.524

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9131	0.087
17DAP/reference	0.98425	0.737
27DAP/reference	1.01123	0.847
39DAP/reference	1.07815	0.256
41DAP/reference	0.96108	0.341
42DAP/reference	0.95527	0.157
43DAP/reference	1.10648	0.163
47DAP/reference	1.01916	1
52DAP/reference	0.92207	0.237
57DAP/reference	0.9234	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1277	0.728
27DAP/17DAP	0.96235	0.887
39DAP/27DAP	0.96211	0.775
41DAP/39DAP	0.92151	0.849
42DAP/41DAP	0.74848	0.034
43DAP/42DAP	1.31533	0.086
47DAP/43DAP	1.14001	0.939
52DAP/47DAP	1.00596	0.9
57DAP/52DAP	1.28065	0.414
57DAP/7DAP	1.51865	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00126	0.758
17DAP/reference	1.01247	0.971
27DAP/reference	0.95307	0.248
39DAP/reference	1.2775	0.009
41DAP/reference	1.20603	0.086
42DAP/reference	1.36702	0.018
43DAP/reference	1.03321	0.802
47DAP/reference	1.12712	0.504
52DAP/reference	0.9927	0.621
57DAP/reference	0.94149	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10602	0.304
17DAP/reference	1.09948	0.303
27DAP/reference	1.14811	0.116
39DAP/reference	1.03068	0.956
41DAP/reference	1.01542	1
42DAP/reference	0.94302	0.212
43DAP/reference	1.10523	0.124
47DAP/reference	1.00514	0.79
52DAP/reference	1.24179	0.006
57DAP/reference	1.32711	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99969	0.75
17DAP/reference	1.07956	0.699
27DAP/reference	1.18866	0.042
39DAP/reference	1.67837	0.307
41DAP/reference	1.09935	0.588
42DAP/reference	0.88546	0.287
43DAP/reference	0.90235	0.188
47DAP/reference	0.95052	0.383
52DAP/reference	0.81492	0.109
57DAP/reference	0.94516	0.283

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9799	1
26DAP/20DAP	1.63317	0.187
34DAP/26DAP	0.83926	0.419
51DAP/34DAP	1.07116	0.936
52DAP/51DAP	1.39457	0.06
53DAP/52DAP	1.12542	0.961
55DAP/53DAP	1.41895	0.075
57DAP/55DAP	1.00822	0.953
62DAP/57DAP	0.88843	0.994
68DAP/62DAP	0.97861	0.863
68DAP/14DAP	1.8415	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68147	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09125	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.68631	0.05
Ripe Pepper/Ripe Tomato	1.7884
Mature Eggplant/Ripe Tomato	4.09746

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.1132
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	N/A	N/A
5-3/M82	1.01389	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	0.83395	0.243
IL2-6/WTpooled	1.01528	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82786	0.31
IL12-4/WTpooled	0.95619	1
IL1-4/WTpooled	0.80409	0.457
WT/WTpooled	1.0921	0.789

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	0.90522	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10572	0.692
DC3000/delta hrp 6h	0.90829	0.95
DC3000/delta hrp 12h	0.88472	1
DC3000/delta hrp 24h	1.13837	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01144
DC3000 delta B/DC3000 delta AB	0.81311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81631	1
Exp 36h	0.79667	0.449
Exp 60h	0.55556	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01457	1
Var 0h	1.42878	0.936
Var 12h I row2-row1	1.00742	0.544
Var 12h NI row2-row1	1.27387	0.34
Var 36h I row2-row1	0.96808	0.805
Var 36h NI row2-row1	0.73967	1
Var 60h I row2-row1	0.86804	0.582
Var 60h NI row2-row1	1.46599	0.904
Time course 0hI-0hNI	0.96562	0.835
Time course 12hI-12hNI	1.23624	0.12
Time course 36hI-36hNI	0.80337	0.023
Time course 60hI-60hNI	0.83744	0.047

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)	0.83039	0.314
transgenic ySAMdc/azygous control (breaker)	0.84278	0.49
transgenic ySAMdc/azygous control (red)	1.05298	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01901	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38311	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86719	1
Manapal/WT (break)	0.91795	1
Manapal/WT (red)	0.46521	0.229