Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84155	0.318
27DAP/17DAP	1.06532	0.881
39DAP/27DAP	1.13396	0.946
41DAP/39DAP	1.32959	0.386
42DAP/41DAP	0.95103	1
43DAP/42DAP	0.96894	0.9
47DAP/43DAP	0.93292	0.754
52DAP/47DAP	1.11134	0.784
57DAP/52DAP	0.86799	0.72

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0348	0.638
17DAP/reference	1.07551	0.138
27DAP/reference	1.03984	0.384
39DAP/reference	1.05077	0.072
41DAP/reference	1.09072	0.093
42DAP/reference	1.02015	0.467
43DAP/reference	0.99611	0.882
47DAP/reference	1.05765	0.148
52DAP/reference	1.07014	0.43
57DAP/reference	0.96917	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90701	0.245
27DAP/17DAP	1.0659	0.831
39DAP/27DAP	0.93206	0.437
41DAP/39DAP	1.11368	0.612
42DAP/41DAP	0.98905	0.835
43DAP/42DAP	0.99165	0.928
47DAP/43DAP	1.17781	0.508
52DAP/47DAP	0.89648	0.498
57DAP/52DAP	0.96936	0.7
57DAP/7DAP	1.13029	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86516	0.146
17DAP/reference	0.734	0.025
27DAP/reference	0.8293	0.022
39DAP/reference	0.7228	0.011
41DAP/reference	0.75787	0.022
42DAP/reference	0.6589	0.01
43DAP/reference	0.73529	0.022
47DAP/reference	0.87066	0.05
52DAP/reference	0.81912	0.04
57DAP/reference	0.83209	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02281	0.915
17DAP/reference	1.05406	0.484
27DAP/reference	0.95609	0.438
39DAP/reference	0.99586	0.642
41DAP/reference	0.91891	0.085
42DAP/reference	0.90507	0.169
43DAP/reference	0.94179	0.25
47DAP/reference	1.06328	0.321
52DAP/reference	1.03356	0.498
57DAP/reference	1.04244	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81469	0.068
17DAP/reference	0.9698	0.615
27DAP/reference	0.80371	0.044
39DAP/reference	0.78952	0.025
41DAP/reference	0.77806	0.025
42DAP/reference	0.75205	0.041
43DAP/reference	0.9104	0.197
47DAP/reference	0.89609	0.069
52DAP/reference	0.76089	0.211
57DAP/reference	0.63141	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92271	0.961
26DAP/20DAP	0.74977	0.512
34DAP/26DAP	0.92392	0.596
51DAP/34DAP	1.03586	0.869
52DAP/51DAP	1.3136	0.063
53DAP/52DAP	0.9495	0.649
55DAP/53DAP	1.001	0.964
57DAP/55DAP	0.93692	0.688
62DAP/57DAP	1.03567	0.868
68DAP/62DAP	0.95392	0.787
68DAP/14DAP	0.90333	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.14033	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.31879	N/A
Mature Green Tomato/Ripe Tomato	0.77238	0.287
Immature Eggplant/Mature Eggplant	0.45316	0.063
Ripe Pepper/Ripe Tomato	0.58266	1
Mature Eggplant/Ripe Tomato	1.07218	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87063	N/A
1-1-2/M82	1.21374	0.977
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	1.05723	N/A
2-1-1/M82	1.71532	N/A
2-1/M82	N/A	N/A
2-6/M82	1.15099	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.78655	0.737
4-3-2/M82	1.14202	1
4-3/M82	N/A	N/A
5-3/M82	0.90281	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.77219	N/A
9-3-2/M82	1.24779	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.9419	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96005	1
IL12-4/WTpooled	1.05337	0.785
IL1-4/WTpooled	0.94903	N/A
WT/WTpooled	0.93723	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	0.98906	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92383	1
DC3000/delta hrp 6h	0.75967	0.874
DC3000/delta hrp 12h	1.025	1
DC3000/delta hrp 24h	1.09217	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37343	0.087
DC3000 delta B/DC3000 delta AB	1.09923	0.377

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0912	1
Exp 36h	1.22689	1
Exp 60h	0.99337	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00076	1
Var 0h	0.9131	0.933
Var 12h I row2-row1	1.076	0.204
Var 12h NI row2-row1	0.98293	0.906
Var 36h I row2-row1	1.02524	1
Var 36h NI row2-row1	0.87516	0.469
Var 60h I row2-row1	0.76599	0.374
Var 60h NI row2-row1	0.88765	0.572
Time course 0hI-0hNI	1.03838	0.662
Time course 12hI-12hNI	1.04863	0.409
Time course 36hI-36hNI	1.4897	0.008
Time course 60hI-60hNI	3.2036	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)	1.25297	0.289
transgenic ySAMdc/azygous control (breaker)	0.56878	0.15
transgenic ySAMdc/azygous control (red)	0.97978	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99599	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69677	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85493	1
Manapal/WT (break)	1.09359	1
Manapal/WT (red)	1.09314	0.413