Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.2.18.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26773	0.403
27DAP/17DAP	1.03156	1
39DAP/27DAP	0.85361	0.487
41DAP/39DAP	1.03721	0.904
42DAP/41DAP	1.04047	0.983
43DAP/42DAP	1.32392	0.569
47DAP/43DAP	1.4358	0.52
52DAP/47DAP	0.93142	0.769
57DAP/52DAP	1.22887	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09244	0.32
17DAP/reference	0.95588	0.278
27DAP/reference	1.00566	1
39DAP/reference	1.09804	0.368
41DAP/reference	1.04552	0.516
42DAP/reference	1.03996	1
43DAP/reference	0.93158	0.135
47DAP/reference	1.05128	0.463
52DAP/reference	0.98552	0.58
57DAP/reference	0.7641	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99931	0.871
27DAP/17DAP	0.94105	0.684
39DAP/27DAP	1.09323	0.483
41DAP/39DAP	1.01384	1
42DAP/41DAP	0.97542	0.759
43DAP/42DAP	1.0653	0.513
47DAP/43DAP	1.05476	0.749
52DAP/47DAP	1.04278	0.835
57DAP/52DAP	1.11638	0.414
57DAP/7DAP	0.90084	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04884	1
17DAP/reference	0.95615	0.389
27DAP/reference	1.05726	0.551
39DAP/reference	0.84004	0.073
41DAP/reference	1.04558	0.811
42DAP/reference	0.97793	0.554
43DAP/reference	0.94576	0.368
47DAP/reference	0.79372	0.222
52DAP/reference	1.00876	0.74
57DAP/reference	1.01918	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2268	0.144
17DAP/reference	1.08228	0.599
27DAP/reference	1.10822	0.488
39DAP/reference	0.97017	0.497
41DAP/reference	1.07856	1
42DAP/reference	1.05857	0.951
43DAP/reference	1.08149	0.688
47DAP/reference	0.99496	0.678
52DAP/reference	1.07852	0.559
57DAP/reference	1.20851	0.155

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9211	0.391
17DAP/reference	0.82684	0.109
27DAP/reference	0.92361	0.286
39DAP/reference	0.93713	0.246
41DAP/reference	0.83966	0.096
42DAP/reference	0.80799	0.049
43DAP/reference	0.921	0.365
47DAP/reference	1.03783	0.901
52DAP/reference	1.98642	0.377
57DAP/reference	1.14132	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97019	1
26DAP/20DAP	0.79286	0.512
34DAP/26DAP	1.13133	1
51DAP/34DAP	1.19418	0.084
52DAP/51DAP	0.98631	1
53DAP/52DAP	1.17385	0.284
55DAP/53DAP	1.15238	0.361
57DAP/55DAP	1.1822	0.955
62DAP/57DAP	1.07959	0.678
68DAP/62DAP	1.12466	0.767
68DAP/14DAP	1.26741	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74952	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.40169	0.08
Mature Green Tomato/Ripe Tomato	0.86943	0.317
Immature Eggplant/Mature Eggplant	1.83897	0.054
Ripe Pepper/Ripe Tomato	3.92204	0.258
Mature Eggplant/Ripe Tomato	0.59628	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.66908	N/A
12-2/M82	N/A	N/A
12-4/M82	0.77364	0.619
1-3/M82	0.75382	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.18267	0.395
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	0.92989	1
4-3/M82	N/A	N/A
5-3/M82	0.8346	0.642
6-2/M82	N/A	N/A
6-3/M82	1.25459	N/A
7-1/M82	0.89674	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.91481	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21423	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05595	N/A
IL12-4/WTpooled	1.23712	0.538
IL1-4/WTpooled	1.10838	1
WT/WTpooled	1.04858	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	1.38256	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16252	0.921
DC3000/delta hrp 6h	0.90651	0.95
DC3000/delta hrp 12h	1.06366	1
DC3000/delta hrp 24h	1.47665	0.232

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2985	0.073
DC3000 delta B/DC3000 delta AB	0.94428	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.25769	1
Exp 60h	1.12803	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9837	1
Var 0h	0.92799	1
Var 12h I row2-row1	1.00222	1
Var 12h NI row2-row1	0.94122	0.82
Var 36h I row2-row1	1.03595	1
Var 36h NI row2-row1	0.96948	0.791
Var 60h I row2-row1	0.87957	0.285
Var 60h NI row2-row1	1.03388	1
Time course 0hI-0hNI	1.00104	1
Time course 12hI-12hNI	1.04265	0.672
Time course 36hI-36hNI	1.25011	0.07
Time course 60hI-60hNI	2.90892	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)	0.91514	0.567
transgenic ySAMdc/azygous control (breaker)	0.67117	0.139
transgenic ySAMdc/azygous control (red)	1.08454	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06485	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59741	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.30684	0.14
Manapal/WT (break)	1.6863	0.183
Manapal/WT (red)	1.70875	0.413