Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.6.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25586	0.428
27DAP/17DAP	1.18393	0.88
39DAP/27DAP	1.30934	0.307
41DAP/39DAP	0.99047	0.919
42DAP/41DAP	1.34043	0.556
43DAP/42DAP	0.91103	0.708
47DAP/43DAP	1.25179	0.412
52DAP/47DAP	0.96615	0.758
57DAP/52DAP	1.01912	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9643	0.476
17DAP/reference	1.03676	0.33
27DAP/reference	0.95834	0.275
39DAP/reference	0.99028	0.841
41DAP/reference	1.02479	0.48
42DAP/reference	0.92396	0.038
43DAP/reference	1.04187	0.445
47DAP/reference	1.00969	1
52DAP/reference	0.82825	0.115
57DAP/reference	0.80221	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0961	0.762
27DAP/17DAP	0.94146	0.878
39DAP/27DAP	1.29999	0.347
41DAP/39DAP	0.75076	0.121
42DAP/41DAP	1.22736	0.327
43DAP/42DAP	1.00025	0.875
47DAP/43DAP	1.19923	0.05
52DAP/47DAP	1.7125	0.09
57DAP/52DAP	1.41968	0.159
57DAP/7DAP	1.27272	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92436	0.246
17DAP/reference	0.95028	0.389
27DAP/reference	1.10804	0.664
39DAP/reference	1.05357	1
41DAP/reference	1.12541	0.507
42DAP/reference	1.21582	0.686
43DAP/reference	1.16142	0.603
47DAP/reference	1.13807	0.304
52DAP/reference	1.27308	0.523
57DAP/reference	0.98751	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10302	0.294
17DAP/reference	0.99876	0.805
27DAP/reference	0.97751	0.537
39DAP/reference	0.87495	0.159
41DAP/reference	0.8944	0.112
42DAP/reference	0.91799	0.098
43DAP/reference	0.93613	0.212
47DAP/reference	1.01009	0.916
52DAP/reference	1.02396	0.789
57DAP/reference	1.25586	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03061	1
17DAP/reference	0.80706	0.328
27DAP/reference	1.11988	0.749
39DAP/reference	1.03138	1
41DAP/reference	1.54193	0.145
42DAP/reference	0.95839	0.671
43DAP/reference	1.28275	0.426
47DAP/reference	0.92808	0.278
52DAP/reference	1.27966	0.324
57DAP/reference	0.89981	0.258

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0633	0.966
26DAP/20DAP	1.55362	0.19
34DAP/26DAP	0.59613	0.189
51DAP/34DAP	2.28304	0.03
52DAP/51DAP	0.71338	1
53DAP/52DAP	2.56425	0.03
55DAP/53DAP	1.01673	0.894
57DAP/55DAP	0.8488	0.37
62DAP/57DAP	0.96036	0.871
68DAP/62DAP	1.04178	0.984
68DAP/14DAP	0.96926	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.02651	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.65739	0.047
Immature Eggplant/Mature Eggplant	1.5904	0.076
Ripe Pepper/Ripe Tomato	0.34089
Mature Eggplant/Ripe Tomato	0.79029	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	1.38329
4-3-2/M82	1.18495
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	0.87258

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9366	0.321
IL2-6/WTpooled	1.01153	1
IL7-5/WTpooled	1.18686	0.792
IL7-3/WTpooled	1.0037	1
IL12-4/WTpooled	1.07497	0.839
IL1-4/WTpooled	1.02523	1
WT/WTpooled	1.0367	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	1.04078	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03395	0.921
DC3000/delta hrp 6h	0.78467	0.95
DC3000/delta hrp 12h	1.28401	1
DC3000/delta hrp 24h	0.41772	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.04765

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98366	1
Exp 36h	1.38295	0.693
Exp 60h	1.20577	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01253	1
Var 0h	0.88678	0.933
Var 12h I row2-row1	1.40483	0.296
Var 12h NI row2-row1	1.12097	1
Var 36h I row2-row1	1.04757	1
Var 36h NI row2-row1	1.3659	0.276
Var 60h I row2-row1	0.89722	0.285
Var 60h NI row2-row1	1.26284	0.904
Time course 0hI-0hNI	0.99325	1
Time course 12hI-12hNI	0.97183	0.802
Time course 36hI-36hNI	0.81232	0.023
Time course 60hI-60hNI	0.36516	0.006

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)	1.10977	0.455
transgenic ySAMdc/azygous control (breaker)	0.91103	0.49
transgenic ySAMdc/azygous control (red)	0.88621	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0296	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88015	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96454	1
Manapal/WT (break)	0.92464	1
Manapal/WT (red)	0.99567	0.863