Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.4.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.3447	0.02
27DAP/17DAP	1.82463	0.479
39DAP/27DAP	1.09645	1
41DAP/39DAP	0.73806	0.233
42DAP/41DAP	1.36863	0.772
43DAP/42DAP	0.98981	0.914
47DAP/43DAP	0.71764	0.239
52DAP/47DAP	3.90671	0.02
57DAP/52DAP	0.84442	0.882

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94131	0.379
17DAP/reference	1.03561	0.342
27DAP/reference	1.03486	0.375
39DAP/reference	1.01868	0.434
41DAP/reference	0.979	0.667
42DAP/reference	0.93846	0.085
43DAP/reference	0.93317	0.377
47DAP/reference	0.94156	0.137
52DAP/reference	0.88303	0.143
57DAP/reference	0.88514	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.98131	0.445
27DAP/17DAP	0.84749	0.508
39DAP/27DAP	1.12035	0.611
41DAP/39DAP	1.25194	0.612
42DAP/41DAP	0.84515	0.305
43DAP/42DAP	1.66166	0.024
47DAP/43DAP	0.96577	0.796
52DAP/47DAP	2.01066	0.048
57DAP/52DAP	4.61838	0.029
57DAP/7DAP	2.05526	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78281	0.063
17DAP/reference	1.13454	0.328
27DAP/reference	0.88274	0.171
39DAP/reference	0.8575	0.039
41DAP/reference	1.04747	0.836
42DAP/reference	1.05344	1
43DAP/reference	1.56425	0.013
47DAP/reference	0.93254	0.383
52DAP/reference	1.04209	0.599
57DAP/reference	1.4003	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93946	0.362
17DAP/reference	1.0027	1
27DAP/reference	0.96322	0.452
39DAP/reference	0.85699	0.136
41DAP/reference	1.00981	0.683
42DAP/reference	0.86677	0.089
43DAP/reference	1.08619	0.575
47DAP/reference	1.04377	0.225
52DAP/reference	0.92092	0.023
57DAP/reference	1.05408	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81618	0.054
17DAP/reference	0.92877	0.292
27DAP/reference	0.96696	0.442
39DAP/reference	1.25602	0.018
41DAP/reference	0.92374	0.371
42DAP/reference	0.96999	0.671
43DAP/reference	0.96493	0.545
47DAP/reference	1.10416	0.207
52DAP/reference	1.05877	0.664
57DAP/reference	1.15934	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01367	1
26DAP/20DAP	1.09717	0.798
34DAP/26DAP	1.01984	1
51DAP/34DAP	1.03051	0.949
52DAP/51DAP	2.71798	0.033
53DAP/52DAP	0.39542	0.049
55DAP/53DAP	0.6743	0.03
57DAP/55DAP	1.21191	0.818
62DAP/57DAP	1.76225	0.024
68DAP/62DAP	0.81584	0.668
68DAP/14DAP	1.00358	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.20338	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.25026	0.075
Mature Green Tomato/Ripe Tomato	0.32821	0.017
Immature Eggplant/Mature Eggplant	0.66007	0.092
Ripe Pepper/Ripe Tomato	0.93964	0.293
Mature Eggplant/Ripe Tomato	1.21948	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.44136	N/A
1-1-2/M82	1.01985	1
12-2/M82	6.74422	N/A
12-4/M82	0.92625	1
1-3/M82	0.93542	N/A
2-1-1/M82	0.84681	0.784
2-1/M82	N/A	N/A
2-6/M82	2.48917	0.505
3-2/M82	1.34025	0.967
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	2.03554	1
5-3/M82	0.26202	0.344
6-2/M82	1.37119	N/A
6-3/M82	0.37394	N/A
7-1/M82	1.29778	1
7-2/M82	0.94149	N/A
9-3-2/M82	1.08463	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92441	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.34956	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.89399	0.581
IL1-4/WTpooled	0.96267	1
WT/WTpooled	1.06058	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	0.96098	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13021	0.758
DC3000/delta hrp 6h	0.9886	0.95
DC3000/delta hrp 12h	1.11805	1
DC3000/delta hrp 24h	1.20809	0.082

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25415	0.042
DC3000 delta B/DC3000 delta AB	1.49998	0.19

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07107	1
Exp 36h	1.18348	1
Exp 60h	1.15474	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01082	1
Var 0h	0.93967	0.933
Var 12h I row2-row1	1.2679	0.544
Var 12h NI row2-row1	0.98651	1
Var 36h I row2-row1	1.20411	1
Var 36h NI row2-row1	1.86232	1
Var 60h I row2-row1	0.68725	0.285
Var 60h NI row2-row1	1.01144	1
Time course 0hI-0hNI	1.10202	0.574
Time course 12hI-12hNI	1.10665	0.517
Time course 36hI-36hNI	1.47302	0.005
Time course 60hI-60hNI	1.44495	0.137

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)	1.19238	0.372
transgenic ySAMdc/azygous control (breaker)	0.47101	0.132
transgenic ySAMdc/azygous control (red)	1.57051	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01738	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75092	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88194	1
Manapal/WT (break)	0.6272	0.333
Manapal/WT (red)	1.01718	1