Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84822	0.503
27DAP/17DAP	1.4894	0.552
39DAP/27DAP	0.74456	0.474
41DAP/39DAP	0.97715	0.871
42DAP/41DAP	1.40996	0.434
43DAP/42DAP	0.91943	0.865
47DAP/43DAP	1.18268	0.793
52DAP/47DAP	1.20351	0.873
57DAP/52DAP	1.1939	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8256	0.026
17DAP/reference	0.85599	0.009
27DAP/reference	0.94147	0.395
39DAP/reference	0.90839	0.149
41DAP/reference	0.83575	0.039
42DAP/reference	0.87733	0.009
43DAP/reference	0.91413	0.135
47DAP/reference	0.96849	0.345
52DAP/reference	1.04091	0.84
57DAP/reference	1.13932	0.114

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19385	0.151
27DAP/17DAP	1.2849	0.686
39DAP/27DAP	0.93292	0.601
41DAP/39DAP	1.43109	0.837
42DAP/41DAP	0.97314	0.746
43DAP/42DAP	0.88678	0.415
47DAP/43DAP	1.05234	0.833
52DAP/47DAP	0.92836	0.666
57DAP/52DAP	1.11582	0.504
57DAP/7DAP	0.60302	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18723	0.11
17DAP/reference	1.19566	0.059
27DAP/reference	1.11269	0.664
39DAP/reference	1.08025	1
41DAP/reference	1.09722	0.56
42DAP/reference	1.28342	0.174
43DAP/reference	1.4344	0.066
47DAP/reference	1.54568	0.37
52DAP/reference	1.22828	0.286
57DAP/reference	1.31539	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9131	0.353
17DAP/reference	0.76248	0.009
27DAP/reference	0.78501	0.023
39DAP/reference	1.03645	0.868
41DAP/reference	0.96965	0.432
42DAP/reference	0.94748	0.355
43DAP/reference	0.97197	0.569
47DAP/reference	0.91446	0.129
52DAP/reference	0.99601	0.666
57DAP/reference	0.7981	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00148	0.804
17DAP/reference	1.06851	0.746
27DAP/reference	1.28202	0.075
39DAP/reference	1.19046	0.146
41DAP/reference	1.2846	0.112
42DAP/reference	1.09834	0.49
43DAP/reference	1.07935	0.524
47DAP/reference	1.05447	0.562
52DAP/reference	1.0662	0.79
57DAP/reference	1.18556	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08767	0.966
26DAP/20DAP	0.86584	1
34DAP/26DAP	1.12183	1
51DAP/34DAP	0.68909	0.205
52DAP/51DAP	1.34436	0.733
53DAP/52DAP	1.24985	0.138
55DAP/53DAP	0.93387	0.735
57DAP/55DAP	0.77872	0.219
62DAP/57DAP	1.2913	0.833
68DAP/62DAP	1.5108	0.316
68DAP/14DAP	1.98607	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.36251	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	12.9332
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.77725
12-2/M82	N/A	N/A
12-4/M82	0.77713
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.82344	0.642
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02441	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.92848	0.294
IL12-4/WTpooled	0.96524	0.581
IL1-4/WTpooled	0.8133	0.834
WT/WTpooled	1.05406	0.874

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	0.7356

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98076	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.06853	1
DC3000/delta hrp 24h	0.82388	0.319

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	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	0.69884	0.661
Exp 60h	1.01477	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96191	1
Var 0h	0.63536	0.933
Var 12h I row2-row1	0.97391	0.948
Var 12h NI row2-row1	0.98431	1
Var 36h I row2-row1	0.95407	1
Var 36h NI row2-row1	1.11742	1
Var 60h I row2-row1	0.93038	0.832
Var 60h NI row2-row1	1.11984	0.904
Time course 0hI-0hNI	1.04615	0.852
Time course 12hI-12hNI	0.93286	0.711
Time course 36hI-36hNI	0.81584	0.046
Time course 60hI-60hNI	0.56589	0.007

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)	0.96635	0.529
transgenic ySAMdc/azygous control (breaker)	1.43958	0.178
transgenic ySAMdc/azygous control (red)	1.16523	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02617	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97281	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47495	0.096
Manapal/WT (break)	1.47936	0.183
Manapal/WT (red)	1.31468	0.222