Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.14.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83277	0.364
27DAP/17DAP	0.89179	0.751
39DAP/27DAP	1.70121	0.126
41DAP/39DAP	1.21499	0.642
42DAP/41DAP	0.82468	0.774
43DAP/42DAP	1.10382	1
47DAP/43DAP	0.94025	0.773
52DAP/47DAP	1.65306	0.196
57DAP/52DAP	0.98876	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26636	0.065
17DAP/reference	0.78097	0.085
27DAP/reference	0.81316	0.163
39DAP/reference	0.83715	0.213
41DAP/reference	0.80752	0.267
42DAP/reference	1.07414	0.656
43DAP/reference	0.8876	0.18
47DAP/reference	1.05759	0.937
52DAP/reference	1.01197	0.689
57DAP/reference	1.03521	0.783

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63026	0.065
27DAP/17DAP	1.22515	0.353
39DAP/27DAP	1.0435	0.799
41DAP/39DAP	1.202	0.565
42DAP/41DAP	1.16676	0.327
43DAP/42DAP	0.89535	0.149
47DAP/43DAP	1.26526	0.157
52DAP/47DAP	0.85118	0.284
57DAP/52DAP	1.11475	0.666
57DAP/7DAP	1.00256	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81031	0.138
17DAP/reference	0.61124	0.013
27DAP/reference	0.65839	0.01
39DAP/reference	0.60308	0.012
41DAP/reference	0.64378	0.023
42DAP/reference	0.57703	0.01
43DAP/reference	0.69721	0.015
47DAP/reference	1.12146	0.732
52DAP/reference	0.6599	0.012
57DAP/reference	0.79131	0.059

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15231	0.35
17DAP/reference	0.99884	0.711
27DAP/reference	1.29143	0.118
39DAP/reference	1.03186	1
41DAP/reference	1.15806	0.157
42DAP/reference	1.09491	0.38
43DAP/reference	0.77897	0.144
47DAP/reference	0.98005	0.459
52DAP/reference	0.75274	0.04
57DAP/reference	0.75873	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82498	0.042
17DAP/reference	0.85059	0.198
27DAP/reference	0.78862	0.042
39DAP/reference	0.88126	0.083
41DAP/reference	0.72868	0.02
42DAP/reference	0.71334	0.028
43DAP/reference	0.86842	0.197
47DAP/reference	0.87255	0.207
52DAP/reference	1.09506	0.941
57DAP/reference	0.95884	0.534

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00931	1
26DAP/20DAP	0.68219	0.244
34DAP/26DAP	2.38193
51DAP/34DAP	1.25713	0.967
52DAP/51DAP	0.98847	1
53DAP/52DAP	2.39849	0.502
55DAP/53DAP	1.23364	0.908
57DAP/55DAP	1.22179	0.935
62DAP/57DAP	0.72547	0.088
68DAP/62DAP	1.31704	0.95
68DAP/14DAP	1.03406	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30026	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.44329	0.081
Mature Green Tomato/Ripe Tomato	0.65824	0.028
Immature Eggplant/Mature Eggplant	1.0705	0.248
Ripe Pepper/Ripe Tomato	0.93515	1
Mature Eggplant/Ripe Tomato	0.31684	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.6147	0.605
1-1-2/M82	1.08324	1
12-2/M82	1.00954	1
12-4/M82	0.8474
1-3/M82	1.31546	0.479
2-1-1/M82	0.87658	1
2-1/M82	1.05612	1
2-6/M82	0.85065	1
3-2/M82	0.62354	0.455
4-1-1/M82	0.81796	1
4-1/M82	0.68896	0.737
4-3-2/M82	0.83265	0.698
4-3/M82	0.73623	0.578
5-3/M82	1.24335	0.572
6-2/M82	1.14343	1
6-3/M82	0.97405	1
7-1/M82	1.09573	1
7-2/M82	1.13888	1
9-3-2/M82	0.79939	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77536	0.247
IL2-6/WTpooled	1.00971	1
IL7-5/WTpooled	0.86998	1
IL7-3/WTpooled	0.9447	1
IL12-4/WTpooled	0.93947	1
IL1-4/WTpooled	1.03187	1
WT/WTpooled	1.00761	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	1.59683	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02247	1
DC3000/delta hrp 6h	1.02651	1
DC3000/delta hrp 12h	1.33985	1
DC3000/delta hrp 24h	1.00187	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50395	0.27
DC3000 delta B/DC3000 delta AB	2.00988	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13758	1
Exp 36h	1.1125	1
Exp 60h	1.28835	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99841	1
Var 0h	1.13615	0.289
Var 12h I row2-row1	0.83299	0.418
Var 12h NI row2-row1	1.03359	1
Var 36h I row2-row1	1.25164	0.309
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.68199
Var 60h NI row2-row1	0.80368	0.302
Time course 0hI-0hNI	1.23995	0.662
Time course 12hI-12hNI	1.03115	0.818
Time course 36hI-36hNI	1.43487	0.009
Time course 60hI-60hNI	2.88287	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)	1.20321	0.238
transgenic ySAMdc/azygous control (breaker)	0.88246	0.49
transgenic ySAMdc/azygous control (red)	0.77224	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24733	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.36418	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01146	1
Manapal/WT (break)	0.73911	0.333
Manapal/WT (red)	0.75049	0.184