Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83031	0.324
27DAP/17DAP	1.22251	0.799
39DAP/27DAP	0.72629	0.402
41DAP/39DAP	1.07604	0.685
42DAP/41DAP	1.24222	0.772
43DAP/42DAP	0.87668	0.77
47DAP/43DAP	1.22013	0.459
52DAP/47DAP	1.14568	0.721
57DAP/52DAP	1.12008	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00658	1
17DAP/reference	1.0499	0.258
27DAP/reference	1.0114	0.806
39DAP/reference	0.98902	0.828
41DAP/reference	1.0086	0.91
42DAP/reference	0.93575	0.025
43DAP/reference	0.91678	0.17
47DAP/reference	0.95161	0.116
52DAP/reference	0.97864	0.504
57DAP/reference	0.86872	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02417	0.91
27DAP/17DAP	1.03218	0.9
39DAP/27DAP	0.98856	0.932
41DAP/39DAP	1.09366	0.682
42DAP/41DAP	1.03018	0.773
43DAP/42DAP	0.91157	0.06
47DAP/43DAP	0.94701	0.499
52DAP/47DAP	0.9915	0.935
57DAP/52DAP	1.00864	1
57DAP/7DAP	1.03914	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33569	0.263
17DAP/reference	2.84758	0.006
27DAP/reference	2.11615	0.007
39DAP/reference	2.83129	0.005
41DAP/reference	3.01963	0.011
42DAP/reference	3.18742	0.006
43DAP/reference	4.07986	0.007
47DAP/reference	2.05105	0.106
52DAP/reference	2.69224	0.007
57DAP/reference	2.19799	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03749	0.612
17DAP/reference	1.03124	0.367
27DAP/reference	0.96855	0.452
39DAP/reference	0.99505	0.661
41DAP/reference	0.97689	0.481
42DAP/reference	0.96658	0.321
43DAP/reference	0.95142	0.438
47DAP/reference	0.92799	0.016
52DAP/reference	1.00948	1
57DAP/reference	1.08052	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66245	0.019
17DAP/reference	1.50898	0.326
27DAP/reference	3.04356	0.02
39DAP/reference	2.73506	0.007
41DAP/reference	2.15875	0.016
42DAP/reference	2.37254	0.01
43DAP/reference	1.80281	0.139
47DAP/reference	1.04973	0.461
52DAP/reference	3.38346	0.038
57DAP/reference	1.84334	0.511

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99168	1
26DAP/20DAP	0.98472	1
34DAP/26DAP	1.00537	1
51DAP/34DAP	0.89703	0.328
52DAP/51DAP	0.99885	1
53DAP/52DAP	1.01087	0.91
55DAP/53DAP	0.99973	0.917
57DAP/55DAP	1.15502	0.666
62DAP/57DAP	1.15709	0.393
68DAP/62DAP	0.96425	0.81
68DAP/14DAP	1.18995	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91414	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.54032	0.068
Mature Green Tomato/Ripe Tomato	2.76658	0.028
Immature Eggplant/Mature Eggplant	0.77395	0.071
Ripe Pepper/Ripe Tomato	2.99742	1
Mature Eggplant/Ripe Tomato	2.00982

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0661	1
1-1-2/M82	0.93393	1
12-2/M82	1.08272	1
12-4/M82	0.81516	1
1-3/M82	0.85085	0.441
2-1-1/M82	1.03098	0.764
2-1/M82	1.32502	0.312
2-6/M82	0.97813	1
3-2/M82	1.02803	0.967
4-1-1/M82	0.90831	1
4-1/M82	1.15281	0.853
4-3-2/M82	0.91993	1
4-3/M82	1.07347	1
5-3/M82	1.00342	1
6-2/M82	1.00459	1
6-3/M82	1.01793	1
7-1/M82	0.90929
7-2/M82	1.01203	1
9-3-2/M82	0.70635

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86939	1
IL2-6/WTpooled	1.31077	0.584
IL7-5/WTpooled	0.74562	1
IL7-3/WTpooled	1.25194	1
IL12-4/WTpooled	1.04902	0.532
IL1-4/WTpooled	0.80822	0.834
WT/WTpooled	1.07652	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	0.79506

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09326	0.774
DC3000/delta hrp 6h	1.26222	0.857
DC3000/delta hrp 12h	1.04359	1
DC3000/delta hrp 24h	1.06308	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16945	0.094
DC3000 delta B/DC3000 delta AB	1.08119	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20686	1
Exp 36h	0.74114	0.749
Exp 60h	1.10129	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02512	1
Var 0h	1.10518	0.936
Var 12h I row2-row1	1.08042	0.613
Var 12h NI row2-row1	1.09866	1
Var 36h I row2-row1	0.97824	1
Var 36h NI row2-row1	0.8867	0.549
Var 60h I row2-row1	0.96017	0.285
Var 60h NI row2-row1	1.22969	0.904
Time course 0hI-0hNI	1.15415	0.662
Time course 12hI-12hNI	1.03286	0.82
Time course 36hI-36hNI	1.01015	0.975
Time course 60hI-60hNI	1.40838	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)	1.1988	0.431
transgenic ySAMdc/azygous control (breaker)	1.12188	1
transgenic ySAMdc/azygous control (red)	0.81056	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02666	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82735	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22332	1
Manapal/WT (break)	0.8308	0.299
Manapal/WT (red)	0.61552	0.181