Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.18.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00561	0.858
27DAP/17DAP	1.35249	0.681
39DAP/27DAP	0.82119	0.529
41DAP/39DAP	0.91586	0.772
42DAP/41DAP	1.2865	0.449
43DAP/42DAP	1.1171	1
47DAP/43DAP	0.95309	0.804
52DAP/47DAP	1.03827	0.964
57DAP/52DAP	1.04277	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0202	0.9
17DAP/reference	1.15649	0.055
27DAP/reference	0.91143	0.052
39DAP/reference	1.10996	0.049
41DAP/reference	1.01879	0.91
42DAP/reference	0.86152	0.01
43DAP/reference	1.06143	0.36
47DAP/reference	0.96749	0.279
52DAP/reference	0.84132	0.118
57DAP/reference	0.83716	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9827	0.763
27DAP/17DAP	1.01619	1
39DAP/27DAP	1.00794	1
41DAP/39DAP	1.13983	0.853
42DAP/41DAP	0.97498	0.772
43DAP/42DAP	1.18551	0.413
47DAP/43DAP	1.01048	0.985
52DAP/47DAP	1.14659	0.57
57DAP/52DAP	1.14822	0.688
57DAP/7DAP	0.87868	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00148	1
17DAP/reference	0.92364	0.192
27DAP/reference	1.27675	0.551
39DAP/reference	0.8892	0.17
41DAP/reference	1.02652	1
42DAP/reference	0.98512	0.554
43DAP/reference	1.12629	0.188
47DAP/reference	0.91932	0.383
52DAP/reference	1.0276	0.941
57DAP/reference	1.23948	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04204	1
17DAP/reference	0.85466	0.129
27DAP/reference	0.85838	0.144
39DAP/reference	0.83624	0.136
41DAP/reference	0.87214	0.13
42DAP/reference	0.71242	0.013
43DAP/reference	1.15771	0.161
47DAP/reference	0.99281	0.643
52DAP/reference	0.8854	0.06
57DAP/reference	1.09269	0.477

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88406	0.197
17DAP/reference	0.89126	0.231
27DAP/reference	0.99961	0.763
39DAP/reference	0.97838	0.591
41DAP/reference	0.98779	0.682
42DAP/reference	0.86398	0.22
43DAP/reference	0.78811	0.188
47DAP/reference	0.8645	0.054
52DAP/reference	1.25844	0.614
57DAP/reference	0.70399	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07186	1
26DAP/20DAP	1.44591	0.325
34DAP/26DAP	1.82753	0.542
51DAP/34DAP	2.60544	0.034
52DAP/51DAP	1.10795	0.873
53DAP/52DAP	1.35946	0.104
55DAP/53DAP	1.09389	0.261
57DAP/55DAP	1.18719	0.793
62DAP/57DAP	1.25322	0.185
68DAP/62DAP	1.2673	0.398
68DAP/14DAP	1.53925	0.179

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56156	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.13658	0.054
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	9.45159
Ripe Pepper/Ripe Tomato	3.23741	1
Mature Eggplant/Ripe Tomato	0.85094	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88739	0.944
1-1-2/M82	1.06445	1
12-2/M82	1.07515
12-4/M82	0.8162	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.75643	0.784
2-1/M82	0.77443
2-6/M82	0.86215	0.501
3-2/M82	1.2015
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	1.03431	1
5-3/M82	1.24099	0.572
6-2/M82	0.79521
6-3/M82	1.04996	1
7-1/M82	N/A	N/A
7-2/M82	0.9269	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9458
IL2-6/WTpooled	1.20513	0.659
IL7-5/WTpooled	0.89363	1
IL7-3/WTpooled	0.95195	1
IL12-4/WTpooled	1.30172	0.737
IL1-4/WTpooled	0.80466
WT/WTpooled	1.085	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	2.19854	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91257	1
DC3000/delta hrp 6h	0.36319
DC3000/delta hrp 12h	1.18198	1
DC3000/delta hrp 24h	1.14396	0.37

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35572
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.27683	0.409
Exp 60h	1.60614	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.54748	1
Var 0h	1.01488	0.98
Var 12h I row2-row1	1.14888	0.204
Var 12h NI row2-row1	1.14979	1
Var 36h I row2-row1	0.97947	1
Var 36h NI row2-row1	0.37689	0.584
Var 60h I row2-row1	0.69444	0.285
Var 60h NI row2-row1	1.21272	0.904
Time course 0hI-0hNI	1.03987	1
Time course 12hI-12hNI	1.83762	0.011
Time course 36hI-36hNI	3.60273	0.004
Time course 60hI-60hNI	11.883	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)	1.2796	0.699
transgenic ySAMdc/azygous control (breaker)	1.0049	1
transgenic ySAMdc/azygous control (red)	1.53302	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05974	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87443	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75005	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.79337	0.274