Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.5.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55695	0.078
27DAP/17DAP	0.85911	0.635
39DAP/27DAP	0.64229	0.399
41DAP/39DAP	0.76191	0.171
42DAP/41DAP	0.73929	0.774
43DAP/42DAP	1.29179	0.553
47DAP/43DAP	0.82806	0.467
52DAP/47DAP	1.00564	0.956
57DAP/52DAP	1.07615	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17377	0.071
17DAP/reference	1.23815	0.086
27DAP/reference	1.32234	0.011
39DAP/reference	1.19454	0.218
41DAP/reference	1.63736	0.012
42DAP/reference	1.95818	0.001
43DAP/reference	1.28072	0.306
47DAP/reference	1.42307	0.027
52DAP/reference	1.49282	0.017
57DAP/reference	1.2106	0.195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.8234	0.036
27DAP/17DAP	1.19634	0.378
39DAP/27DAP	0.65937	0.048
41DAP/39DAP	0.92707	0.645
42DAP/41DAP	0.98622	0.795
43DAP/42DAP	0.73316	0.023
47DAP/43DAP	0.93901	0.554
52DAP/47DAP	1.09695	0.66
57DAP/52DAP	1.16516	0.36
57DAP/7DAP	0.9572	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08377	0.83
17DAP/reference	1.25932	0.18
27DAP/reference	1.14999	0.301
39DAP/reference	1.24329	0.086
41DAP/reference	1.30936	0.034
42DAP/reference	1.49387	0.018
43DAP/reference	1.17769	0.06
47DAP/reference	2.06889	0.026
52DAP/reference	1.35686	0.034
57DAP/reference	1.15438	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06442	0.626
17DAP/reference	1.46998	0.035
27DAP/reference	1.36197	0.071
39DAP/reference	1.4537	0.124
41DAP/reference	1.2101	0.157
42DAP/reference	1.51224	0.007
43DAP/reference	1.24413	0.547
47DAP/reference	1.40044	0.009
52DAP/reference	1.22366	0.046
57DAP/reference	1.43459	0.214

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22495	0.045
17DAP/reference	1.19492	0.148
27DAP/reference	1.08219	0.325
39DAP/reference	1.22861	0.022
41DAP/reference	1.14652	0.222
42DAP/reference	1.60616	0.146
43DAP/reference	1.56892	0.022
47DAP/reference	1.73815	0.007
52DAP/reference	1.28965	0.136
57DAP/reference	1.53815	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7946	0.033
26DAP/20DAP	1.06556	0.813
34DAP/26DAP	1.30445	0.819
51DAP/34DAP	0.9425	0.674
52DAP/51DAP	1.15278	0.358
53DAP/52DAP	0.91489	0.684
55DAP/53DAP	1.02465	1
57DAP/55DAP	1.26767	0.176
62DAP/57DAP	1.20299	0.935
68DAP/62DAP	1.0911
68DAP/14DAP	0.82946	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04637	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81942	0.272
Mature Green Tomato/Ripe Tomato	3.21222	0.015
Immature Eggplant/Mature Eggplant	1.13099	0.334
Ripe Pepper/Ripe Tomato	0.47815	0.224
Mature Eggplant/Ripe Tomato	0.69484

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.40205
12-2/M82	N/A	N/A
12-4/M82	0.89385
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	0.85838	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.08635	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91788	1
IL2-6/WTpooled	0.85545	1
IL7-5/WTpooled	1.05551
IL7-3/WTpooled	0.72722	0.298
IL12-4/WTpooled	0.82986	0.71
IL1-4/WTpooled	0.91421	0.699
WT/WTpooled	0.94231	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	0.9341	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96954	1
DC3000/delta hrp 6h	1.02794	0.95
DC3000/delta hrp 12h	1.2526	1
DC3000/delta hrp 24h	1.37157	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.30223	0.023
DC3000 delta B/DC3000 delta AB	0.38158	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0129	1
Exp 36h	0.83591	0.456
Exp 60h	1.02006	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95785	1
Var 0h	1.02336	1
Var 12h I row2-row1	0.8073	0.344
Var 12h NI row2-row1	0.96503	0.713
Var 36h I row2-row1	0.82238	0.805
Var 36h NI row2-row1	1.18991	0.482
Var 60h I row2-row1	1.52177	0.543
Var 60h NI row2-row1	1.05334	0.904
Time course 0hI-0hNI	0.98463	0.967
Time course 12hI-12hNI	1.04015	0.774
Time course 36hI-36hNI	0.9164	0.112
Time course 60hI-60hNI	0.11251	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)	0.96251	0.662
transgenic ySAMdc/azygous control (breaker)	0.82912	0.49
transgenic ySAMdc/azygous control (red)	1.22338	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13434	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86701	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89464	1
Manapal/WT (break)	0.89865	1
Manapal/WT (red)	0.73434	0.181