Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03787	0.878
27DAP/17DAP	0.97642	1
39DAP/27DAP	0.96257	0.682
41DAP/39DAP	1.15902	0.259
42DAP/41DAP	0.94393	1
43DAP/42DAP	1.02539	1
47DAP/43DAP	1.09029	0.889
52DAP/47DAP	1.03211	0.945
57DAP/52DAP	1.0869	0.72

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98467	0.513
17DAP/reference	1.01474	0.653
27DAP/reference	0.9896	0.694
39DAP/reference	0.96439	0.611
41DAP/reference	1.12505	0.203
42DAP/reference	0.96029	0.095
43DAP/reference	1.01112	0.899
47DAP/reference	0.96128	0.065
52DAP/reference	0.89264	0.147
57DAP/reference	1.02553	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98168	0.663
27DAP/17DAP	1.13319	0.557
39DAP/27DAP	1.00012	1
41DAP/39DAP	0.97605	0.986
42DAP/41DAP	0.9742	0.721
43DAP/42DAP	1.06314	0.664
47DAP/43DAP	0.79568	0.637
52DAP/47DAP	1.05317	0.826
57DAP/52DAP	0.99874	0.905
57DAP/7DAP	0.99398	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86237	0.088
17DAP/reference	0.75521	0.011
27DAP/reference	0.86096	0.055
39DAP/reference	0.88232	0.017
41DAP/reference	0.90011	0.107
42DAP/reference	0.89114	0.031
43DAP/reference	0.88284	0.064
47DAP/reference	0.8711	0.128
52DAP/reference	0.75944	0.012
57DAP/reference	0.74194	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99947	0.93
17DAP/reference	0.96759	0.201
27DAP/reference	1.03993	0.81
39DAP/reference	0.97649	0.298
41DAP/reference	0.96502	0.459
42DAP/reference	1.00732	1
43DAP/reference	0.89688	0.186
47DAP/reference	0.97806	0.328
52DAP/reference	0.99393	0.576
57DAP/reference	1.06106	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77622	0.04
17DAP/reference	0.91246	0.313
27DAP/reference	0.84459	0.065
39DAP/reference	0.87643	0.122
41DAP/reference	0.81774	0.019
42DAP/reference	0.80188	0.019
43DAP/reference	0.9365	0.095
47DAP/reference	0.99329	0.646
52DAP/reference	1.07093	0.583
57DAP/reference	1.10627	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99804	1
26DAP/20DAP	1.41648	0.17
34DAP/26DAP	0.90324	0.619
51DAP/34DAP	1.13028	0.416
52DAP/51DAP	1.02935	0.783
53DAP/52DAP	0.77617	0.604
55DAP/53DAP	0.9291	0.376
57DAP/55DAP	1.01386	0.94
62DAP/57DAP	0.90879	0.681
68DAP/62DAP	1.06427	0.827
68DAP/14DAP	1.22364	0.125

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73639	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97147	0.726
Mature Green Tomato/Ripe Tomato	1.08014	0.363
Immature Eggplant/Mature Eggplant	1.19509	0.165
Ripe Pepper/Ripe Tomato	6.73758	1
Mature Eggplant/Ripe Tomato	3.70157	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96153	0.944
1-1-2/M82	0.89589	1
12-2/M82	0.93096	0.955
12-4/M82	0.92568	1
1-3/M82	0.97017	1
2-1-1/M82	0.93412	0.465
2-1/M82	1.21744	1
2-6/M82	0.96295	1
3-2/M82	0.85077	0.752
4-1-1/M82	0.98767	1
4-1/M82	0.94449	1
4-3-2/M82	0.8652	0.487
4-3/M82	0.97709	1
5-3/M82	1.04221	1
6-2/M82	0.9854	1
6-3/M82	1.01387	1
7-1/M82	1.04714	1
7-2/M82	0.97146	0.881
9-3-2/M82	0.86842	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97777	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03743	1
IL12-4/WTpooled	0.99961	1
IL1-4/WTpooled	1.10084	1
WT/WTpooled	0.95239	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	1.11248	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01765	0.921
DC3000/delta hrp 6h	1.16075	1
DC3000/delta hrp 12h	0.98255	1
DC3000/delta hrp 24h	0.99955	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16782	0.229
DC3000 delta B/DC3000 delta AB	1.23822	0.193

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16555	1
Exp 36h	2.17139	1
Exp 60h	1.4585	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97771	1
Var 0h	0.68187	1
Var 12h I row2-row1	1.17224	0.263
Var 12h NI row2-row1	0.96338	0.713
Var 36h I row2-row1	1.0929	1
Var 36h NI row2-row1	1.06762	1
Var 60h I row2-row1	1.06151	1
Var 60h NI row2-row1	1.20425	0.904
Time course 0hI-0hNI	0.9907	1
Time course 12hI-12hNI	1.14902	0.035
Time course 36hI-36hNI	1.3784	0.005
Time course 60hI-60hNI	1.08719	0.16

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)	1.1909	0.261
transgenic ySAMdc/azygous control (breaker)	1.29195	1
transgenic ySAMdc/azygous control (red)	1.09416	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95633	0.081

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72103	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69624	0.172
Manapal/WT (break)	1.19595	0.381
Manapal/WT (red)	0.90215	0.503