Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9427	0.652
27DAP/17DAP	0.88138	0.704
39DAP/27DAP	0.70875	0.298
41DAP/39DAP	1.10382	0.691
42DAP/41DAP	1.0093	1
43DAP/42DAP	1.58511	0.071
47DAP/43DAP	0.68233	0.156
52DAP/47DAP	1.46293	0.444
57DAP/52DAP	1.04898	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79331	0.024
17DAP/reference	0.78024	0.021
27DAP/reference	0.9412	0.471
39DAP/reference	0.77464	0.014
41DAP/reference	0.76191	0.013
42DAP/reference	0.91877	0.069
43DAP/reference	0.87425	0.039
47DAP/reference	0.97883	0.445
52DAP/reference	1.32434	0.053
57DAP/reference	1.34685	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17637	0.192
27DAP/17DAP	1.03747	0.881
39DAP/27DAP	0.88118	0.173
41DAP/39DAP	0.9941	1
42DAP/41DAP	1.05266	0.651
43DAP/42DAP	1.24072	0.094
47DAP/43DAP	1.12608	0.131
52DAP/47DAP	1.04186	0.868
57DAP/52DAP	0.98782	0.823
57DAP/7DAP	0.95137	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90473	0.066
17DAP/reference	0.97302	0.447
27DAP/reference	0.954	0.283
39DAP/reference	0.86324	0.073
41DAP/reference	0.81763	0.047
42DAP/reference	0.77164	0.048
43DAP/reference	1.10929	0.603
47DAP/reference	0.93808	0.293
52DAP/reference	1.00326	1
57DAP/reference	0.99791	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97029	0.655
17DAP/reference	0.77027	0.041
27DAP/reference	0.94379	0.257
39DAP/reference	0.98735	0.569
41DAP/reference	1.04569	0.862
42DAP/reference	0.97744	0.534
43DAP/reference	1.01617	0.706
47DAP/reference	0.84496	0.04
52DAP/reference	0.95739	0.051
57DAP/reference	0.84459	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87963	0.127
17DAP/reference	0.92368	0.477
27DAP/reference	0.88854
39DAP/reference	1.01556	0.935
41DAP/reference	0.85069	0.107
42DAP/reference	1.03541	0.877
43DAP/reference	1.02387	0.858
47DAP/reference	0.91164	0.249
52DAP/reference	0.88848	0.351
57DAP/reference	1.33844	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02179	1
26DAP/20DAP	0.97567	1
34DAP/26DAP	1.23461	0.154
51DAP/34DAP	1.03569	0.949
52DAP/51DAP	1.28884	0.035
53DAP/52DAP	0.93061	0.595
55DAP/53DAP	1.1085	0.589
57DAP/55DAP	0.78492	0.097
62DAP/57DAP	1.98985	0.158
68DAP/62DAP	1.59251	0.036
68DAP/14DAP	1.94436	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83931	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86438	0.377
Mature Green Tomato/Ripe Tomato	1.1953	0.577
Immature Eggplant/Mature Eggplant	1.24846	0.165
Ripe Pepper/Ripe Tomato	0.91539	1
Mature Eggplant/Ripe Tomato	0.86583	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06756	1
1-1-2/M82	1.03742	1
12-2/M82	1.30874	0.336
12-4/M82	1.1032	0.655
1-3/M82	1.21332	0.479
2-1-1/M82	0.86788	0.784
2-1/M82	1.06675	1
2-6/M82	0.89271	1
3-2/M82	1.2487
4-1-1/M82	1.01348	1
4-1/M82	1.13776
4-3-2/M82	0.89806
4-3/M82	1.13854	1
5-3/M82	1.03922	1
6-2/M82	1.29793	0.253
6-3/M82	1.11074	1
7-1/M82	1.11162
7-2/M82	0.80544	0.486
9-3-2/M82	0.84425

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.40011
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.48143
IL1-4/WTpooled	1.74249	0.426
WT/WTpooled	0.75652

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	0.78121	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18461	0.692
DC3000/delta hrp 6h	1.0412	1
DC3000/delta hrp 12h	1.0677	1
DC3000/delta hrp 24h	0.9252	0.43

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68845	0.024
DC3000 delta B/DC3000 delta AB	0.76384	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86101	1
Exp 36h	1.33865	0.693
Exp 60h	1.2095	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96859	1
Var 0h	0.47665	0.202
Var 12h I row2-row1	0.7164	0.338
Var 12h NI row2-row1	1.16253	0.649
Var 36h I row2-row1	1.05033	0.742
Var 36h NI row2-row1	1.00847	1
Var 60h I row2-row1	0.9472	0.952
Var 60h NI row2-row1	0.98814	1
Time course 0hI-0hNI	1.0189	1
Time course 12hI-12hNI	0.91544	0.377
Time course 36hI-36hNI	0.84404	0.035
Time course 60hI-60hNI	0.37046	0.005

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)	0.94904	0.3
transgenic ySAMdc/azygous control (breaker)	0.89595	0.49
transgenic ySAMdc/azygous control (red)	1.13703	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03591	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14474	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40342	0.088
Manapal/WT (break)	1.07275	0.381
Manapal/WT (red)	1.12076	0.413