Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36525	0.281
27DAP/17DAP	1.25589	0.804
39DAP/27DAP	1.01037	0.82
41DAP/39DAP	0.97924	0.871
42DAP/41DAP	1.09613	0.938
43DAP/42DAP	1.06623	1
47DAP/43DAP	1.21911	0.595
52DAP/47DAP	1.00968	0.932
57DAP/52DAP	1.04431	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02401	1
17DAP/reference	1.02838	0.858
27DAP/reference	0.96865	0.595
39DAP/reference	1.09149	0.474
41DAP/reference	1.10475	0.047
42DAP/reference	1.22661	0.003
43DAP/reference	0.98375	0.745
47DAP/reference	1.21259	0.002
52DAP/reference	1.18445	0.056
57DAP/reference	1.17378	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9101	0.289
27DAP/17DAP	0.95046	0.58
39DAP/27DAP	1.1376	0.369
41DAP/39DAP	0.98031	0.986
42DAP/41DAP	1.04225	0.824
43DAP/42DAP	1.13029	0.02
47DAP/43DAP	0.98539	0.923
52DAP/47DAP	0.97465	0.876
57DAP/52DAP	1.03784	0.763
57DAP/7DAP	1.03666	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83306	0.095
17DAP/reference	0.76298	0.018
27DAP/reference	0.87089	0.135
39DAP/reference	0.75957	0.011
41DAP/reference	0.84703	0.127
42DAP/reference	0.89362	0.136
43DAP/reference	0.68526	0.016
47DAP/reference	0.96429	0.671
52DAP/reference	0.9882	0.621
57DAP/reference	0.74661	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97384	0.811
17DAP/reference	0.93514	0.389
27DAP/reference	1.06865	0.834
39DAP/reference	1.0621	1
41DAP/reference	1.13126	0.513
42DAP/reference	1.30781	0.108
43DAP/reference	1.12117	0.59
47DAP/reference	1.19703	0.205
52DAP/reference	1.06487	0.838
57DAP/reference	0.9442	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75244	0.034
17DAP/reference	0.93977	0.426
27DAP/reference	0.78335	0.065
39DAP/reference	0.77531	0.014
41DAP/reference	0.97369	0.56
42DAP/reference	0.85528	0.172
43DAP/reference	1.05439	0.734
47DAP/reference	1.00168	0.593
52DAP/reference	0.84974	0.25
57DAP/reference	1.16896	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00584	1
26DAP/20DAP	1.01278	1
34DAP/26DAP	1.06617	1
51DAP/34DAP	0.98178	0.844
52DAP/51DAP	0.89067	0.079
53DAP/52DAP	1.06207	0.83
55DAP/53DAP	1.09474	0.599
57DAP/55DAP	1.1661	0.584
62DAP/57DAP	1.09162	0.935
68DAP/62DAP	0.8149	0.7
68DAP/14DAP	1.42423	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92906	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.92283	0.446
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	0.77959
12-2/M82	N/A	N/A
12-4/M82	1.08532
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	0.97262
4-1-1/M82	N/A	N/A
4-1/M82	1.3334	0.418
4-3-2/M82	0.90352	0.698
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	0.92854
7-2/M82	N/A	N/A
9-3-2/M82	0.86212	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07696
IL12-4/WTpooled	1.1846	0.785
IL1-4/WTpooled	1.06008	1
WT/WTpooled	0.97248	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	0.8748	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.74543	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.36017

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18044	0.145
DC3000 delta B/DC3000 delta AB	1.13799	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96858	1
Var 0h	1.75952	0.98
Var 12h I row2-row1	1.18079	0.204
Var 12h NI row2-row1	1.03124	1
Var 36h I row2-row1	1.07538	1
Var 36h NI row2-row1	0.84269	0.413
Var 60h I row2-row1	1.13397	1
Var 60h NI row2-row1	1.20839	0.904
Time course 0hI-0hNI	0.88971	0.156
Time course 12hI-12hNI	1.04106	0.507
Time course 36hI-36hNI	0.9886	0.654
Time course 60hI-60hNI	1.13621	0.06

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.63727	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.5146	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.88146	1
Manapal/WT (red)	1.71928	0.222