Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9775	0.823
27DAP/17DAP	1.07485	1
39DAP/27DAP	1.35055	0.24
41DAP/39DAP	1.11137	0.806
42DAP/41DAP	1.08507	0.971
43DAP/42DAP	0.96516	0.877
47DAP/43DAP	1.11215	0.965
52DAP/47DAP	0.88972	0.681
57DAP/52DAP	0.74414	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00229	0.63
17DAP/reference	0.88269	0.26
27DAP/reference	1.24295	0.184
39DAP/reference	0.95666	0.6
41DAP/reference	0.97145	0.667
42DAP/reference	1.22972	0.311
43DAP/reference	1.01278	0.861
47DAP/reference	1.49336	0.057
52DAP/reference	1.47848	0.083
57DAP/reference	1.36417	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2862	0.103
27DAP/17DAP	1.13948	0.378
39DAP/27DAP	0.95549	0.732
41DAP/39DAP	1.15227	0.827
42DAP/41DAP	1.02137	1
43DAP/42DAP	0.77454	0.022
47DAP/43DAP	1.01014	0.973
52DAP/47DAP	0.89051	0.572
57DAP/52DAP	1.04046	0.895
57DAP/7DAP	0.86902	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42086	0.049
17DAP/reference	1.29963	0.011
27DAP/reference	1.05936	0.301
39DAP/reference	1.24297	0.016
41DAP/reference	1.15086	0.402
42DAP/reference	1.10595	0.308
43DAP/reference	1.13866	0.167
47DAP/reference	1.32139	0.102
52DAP/reference	1.21336	0.048
57DAP/reference	1.40098	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81396	0.182
17DAP/reference	0.85593	0.239
27DAP/reference	1.18389	0.171
39DAP/reference	1.32561	0.272
41DAP/reference	1.43913	0.06
42DAP/reference	1.27777	0.332
43DAP/reference	0.9565	0.516
47DAP/reference	0.96212	0.446
52DAP/reference	0.94973	0.351
57DAP/reference	0.72532	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31657	0.018
17DAP/reference	1.02303	1
27DAP/reference	1.00012	0.883
39DAP/reference	1.1201	0.084
41DAP/reference	1.08641	0.502
42DAP/reference	1.24176	0.171
43DAP/reference	1.26179	0.062
47DAP/reference	1.21052	0.443
52DAP/reference	1.65236	0.06
57DAP/reference	1.64466	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1611	0.966
26DAP/20DAP	0.94815	1
34DAP/26DAP	0.85068	0.472
51DAP/34DAP	1.01758	1
52DAP/51DAP	1.02136	0.939
53DAP/52DAP	1.30902	0.05
55DAP/53DAP	0.97212	0.784
57DAP/55DAP	1.146	0.906
62DAP/57DAP	1.01034	0.994
68DAP/62DAP	1.16906	0.931
68DAP/14DAP	0.90787

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69448	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80151	0.241
Mature Green Tomato/Ripe Tomato	1.12144	0.752
Immature Eggplant/Mature Eggplant	1.68541	0.165
Ripe Pepper/Ripe Tomato	2.29816	1
Mature Eggplant/Ripe Tomato	1.30268	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11481	1
1-1-2/M82	1.24308	0.977
12-2/M82	0.93808	0.955
12-4/M82	0.95513	1
1-3/M82	1.99257	0.26
2-1-1/M82	1.16079	0.764
2-1/M82	1.21921	1
2-6/M82	0.96579	1
3-2/M82	1.53361
4-1-1/M82	1.08123	1
4-1/M82	1.44375
4-3-2/M82	1.03848	1
4-3/M82	1.3657	0.268
5-3/M82	1.14521	0.572
6-2/M82	0.95362	0.473
6-3/M82	0.96001	1
7-1/M82	0.98085	1
7-2/M82	1.10814	1
9-3-2/M82	1.08552	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90714	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97041	1
IL12-4/WTpooled	1.21775	0.532
IL1-4/WTpooled	1.15716	1
WT/WTpooled	1.10446	0.911

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	0.93867	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07599	0.894
DC3000/delta hrp 6h	0.85767
DC3000/delta hrp 12h	0.91783	1
DC3000/delta hrp 24h	0.98175	0.945

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0759	0.515
DC3000 delta B/DC3000 delta AB	1.09303	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2178	1
Exp 36h	0.54583	0.266
Exp 60h	1.00989	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05048	1
Var 0h	0.89564	0.933
Var 12h I row2-row1	0.86944	0.565
Var 12h NI row2-row1	1.00261	1
Var 36h I row2-row1	1.09712	0.41
Var 36h NI row2-row1	1.15364	1
Var 60h I row2-row1	0.79737	0.285
Var 60h NI row2-row1	0.98138	1
Time course 0hI-0hNI	1.0088	1
Time course 12hI-12hNI	1.02895	0.774
Time course 36hI-36hNI	1.02387	0.799
Time course 60hI-60hNI	0.8836	0.161

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)	0.94364	0.409
transgenic ySAMdc/azygous control (breaker)	0.82279	0.132
transgenic ySAMdc/azygous control (red)	1.00838	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96445	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00942	1
Manapal/WT (break)	1.12429	1
Manapal/WT (red)	1.31354	0.164