Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81526	0.395
27DAP/17DAP	0.88653	0.81
39DAP/27DAP	1.22689	0.658
41DAP/39DAP	1.01985	1
42DAP/41DAP	1.30782	0.863
43DAP/42DAP	0.93471	0.877
47DAP/43DAP	2.80759	0.293
52DAP/47DAP	0.81873	0.581
57DAP/52DAP	1.03541	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93043	0.182
17DAP/reference	1.09776	0.018
27DAP/reference	1.03385	0.721
39DAP/reference	0.90375	0.076
41DAP/reference	1.03702	0.552
42DAP/reference	0.87764	0.009
43DAP/reference	1.02951	0.569
47DAP/reference	0.9252	0.06
52DAP/reference	0.91616	0.172
57DAP/reference	0.80794	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21712	0.091
27DAP/17DAP	0.97975	0.919
39DAP/27DAP	1.13999	0.253
41DAP/39DAP	0.65936	0.08
42DAP/41DAP	1.23596	0.282
43DAP/42DAP	1.13182	0.413
47DAP/43DAP	1.20468	0.218
52DAP/47DAP	0.86107	0.553
57DAP/52DAP	0.7097	0.052
57DAP/7DAP	1.18394	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87386	0.183
17DAP/reference	0.69639	0.012
27DAP/reference	1.00899	0.698
39DAP/reference	1.27068	0.018
41DAP/reference	1.11366	0.524
42DAP/reference	1.10475	0.534
43DAP/reference	1.00531	1
47DAP/reference	0.93185	0.383
52DAP/reference	1.15441	0.308
57DAP/reference	1.21205	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07883	0.767
17DAP/reference	0.99463	0.766
27DAP/reference	0.94145	0.292
39DAP/reference	0.85034	0.087
41DAP/reference	0.8701	0.042
42DAP/reference	0.84192	0.039
43DAP/reference	0.98574	0.681
47DAP/reference	0.85221	0.016
52DAP/reference	1.0319	0.559
57DAP/reference	1.21753	0.091

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06942	0.918
17DAP/reference	0.97927	0.668
27DAP/reference	1.30183	0.059
39DAP/reference	1.0719	0.836
41DAP/reference	1.40188	0.145
42DAP/reference	0.87445	0.445
43DAP/reference	0.97264	0.568
47DAP/reference	0.89817	0.207
52DAP/reference	0.90209	0.242
57DAP/reference	0.59489	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05314	0.945
26DAP/20DAP	0.93957	1
34DAP/26DAP	0.98878	0.94
51DAP/34DAP	0.93972	0.714
52DAP/51DAP	0.83871	1
53DAP/52DAP	0.89596	0.715
55DAP/53DAP	0.66689
57DAP/55DAP	0.67153	0.091
62DAP/57DAP	0.94142	0.871
68DAP/62DAP	0.80841	0.227
68DAP/14DAP	0.80896	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95787	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84145	0.377
Mature Green Tomato/Ripe Tomato	0.94556	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	4.06352	0.256
Mature Eggplant/Ripe Tomato	2.02784

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.83985	0.742
1-1-2/M82	0.89839	1
12-2/M82	0.85854
12-4/M82	1.08929	1
1-3/M82	1.59617
2-1-1/M82	0.55563	0.465
2-1/M82	0.67095
2-6/M82	N/A	N/A
3-2/M82	0.88877	1
4-1-1/M82	0.69933	0.985
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.83199	0.404
5-3/M82	1.38754	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.74659
7-2/M82	0.67658
9-3-2/M82	0.71147

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.0569
IL7-5/WTpooled	1.28667
IL7-3/WTpooled	0.9286	0.418
IL12-4/WTpooled	0.84415	0.581
IL1-4/WTpooled	1.09667	1
WT/WTpooled	0.99946	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	1.46113	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02357	0.914
DC3000/delta hrp 6h	1.0183	0.95
DC3000/delta hrp 12h	1.04112	1
DC3000/delta hrp 24h	0.66401	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.07782
DC3000 delta B/DC3000 delta AB	0.71371

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.92867	0.879
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	1.03306	1
Var 0h	0.71039	1
Var 12h I row2-row1	1.34682	0.196
Var 12h NI row2-row1	1.12222	1
Var 36h I row2-row1	1.1993	1
Var 36h NI row2-row1	1.56905	1
Var 60h I row2-row1	1.05845	0.562
Var 60h NI row2-row1	1.15339	0.904
Time course 0hI-0hNI	0.8675	0.112
Time course 12hI-12hNI	0.99073	0.978
Time course 36hI-36hNI	0.73048	0.023
Time course 60hI-60hNI	0.63227	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)	1.08796	0.286
transgenic ySAMdc/azygous control (breaker)	1.00904	1
transgenic ySAMdc/azygous control (red)	1.06357	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01961	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22316	0.14
Manapal/WT (break)	1.10754	0.381
Manapal/WT (red)	0.73097	0.187