Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.1.9.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94591	0.671
27DAP/17DAP	1.0883	0.892
39DAP/27DAP	1.26491	0.691
41DAP/39DAP	0.88498	0.571
42DAP/41DAP	0.93171	1
43DAP/42DAP	0.80045	0.751
47DAP/43DAP	0.88039	0.609
52DAP/47DAP	1.04	0.946
57DAP/52DAP	1.18579	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83029	0.111
17DAP/reference	0.88703	0.26
27DAP/reference	0.91489	0.339
39DAP/reference	0.9345	0.412
41DAP/reference	0.92561	0.341
42DAP/reference	0.70628	0.004
43DAP/reference	1.03586	0.899
47DAP/reference	0.70177	0.005
52DAP/reference	0.88052	0.099
57DAP/reference	0.94609	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.18843	0.077
27DAP/17DAP	1.21103	0.423
39DAP/27DAP	1.08728	0.728
41DAP/39DAP	1.18966	0.799
42DAP/41DAP	1.19986	0.622
43DAP/42DAP	1.01206	1
47DAP/43DAP	1.07875	0.833
52DAP/47DAP	1.0944	0.785
57DAP/52DAP	1.28627	0.296
57DAP/7DAP	2.52864	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91681	0.138
17DAP/reference	1.03778	0.971
27DAP/reference	0.98474	0.494
39DAP/reference	1.09269	0.486
41DAP/reference	1.05029	0.918
42DAP/reference	0.95032	0.371
43DAP/reference	0.927	0.21
47DAP/reference	0.98169	0.671
52DAP/reference	0.98034	0.571
57DAP/reference	1.04526	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95609	0.639
17DAP/reference	1.18145	0.32
27DAP/reference	0.88467	0.203
39DAP/reference	1.37236	0.686
41DAP/reference	0.95969	0.364
42DAP/reference	0.79158	0.028
43DAP/reference	0.98006	0.646
47DAP/reference	0.94751	0.328
52DAP/reference	0.9959	0.619
57DAP/reference	0.91116	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9901	0.653
17DAP/reference	0.96478	0.592
27DAP/reference	1.00991	1
39DAP/reference	1.0832	0.496
41DAP/reference	1.1269	0.425
42DAP/reference	0.91644	0.445
43DAP/reference	1.07434	1
47DAP/reference	0.8675	0.278
52DAP/reference	1.41307	0.609
57DAP/reference	0.85616	0.093

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04303	1
26DAP/20DAP	1.66786	0.562
34DAP/26DAP	0.88921	0.841
51DAP/34DAP	1.23166	0.473
52DAP/51DAP	0.90653	1
53DAP/52DAP	1.03225	0.944
55DAP/53DAP	2.17659	0.317
57DAP/55DAP	0.68493	0.181
62DAP/57DAP	0.84366	0.088
68DAP/62DAP	0.80977	0.543
68DAP/14DAP	1.637	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9497	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23612	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.08141	N/A
Ripe Pepper/Ripe Tomato	0.8654	0.293
Mature Eggplant/Ripe Tomato	1.93893	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09584	N/A
1-1-2/M82	1.34766	1
12-2/M82	N/A	N/A
12-4/M82	0.84334	0.274
1-3/M82	1.1249	N/A
2-1-1/M82	1.3033	N/A
2-1/M82	1.40685	N/A
2-6/M82	0.93239	N/A
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	1.43622	N/A
4-3/M82	1.16953	1
5-3/M82	0.93385	1
6-2/M82	1.08101	1
6-3/M82	1.00852	1
7-1/M82	0.7618	0.408
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.86321	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07502	1
IL12-4/WTpooled	1.05198	0.737
IL1-4/WTpooled	1.05176	N/A
WT/WTpooled	1.0336	0.713

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	1.04931	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02644	0.921
DC3000/delta hrp 6h	0.82683	0.95
DC3000/delta hrp 12h	1.08287	1
DC3000/delta hrp 24h	1.4051	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.84074	N/A
DC3000 delta B/DC3000 delta AB	1.37888	0.253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03442	1
Exp 36h	0.85845	0.749
Exp 60h	0.95466	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92666	1
Var 0h	1.4264	0.782
Var 12h I row2-row1	0.9141	0.338
Var 12h NI row2-row1	1.26967	0.281
Var 36h I row2-row1	1.16568	0.908
Var 36h NI row2-row1	0.61697	0.469
Var 60h I row2-row1	0.59305	0.439
Var 60h NI row2-row1	1.0033	1
Time course 0hI-0hNI	1.20483	0.189
Time course 12hI-12hNI	0.96644	0.738
Time course 36hI-36hNI	0.97091	0.476
Time course 60hI-60hNI	1.48894	0.013

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)	0.98095	0.722
transgenic ySAMdc/azygous control (breaker)	0.65626	0.137
transgenic ySAMdc/azygous control (red)	1.03743	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98092	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7399	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13046	1
Manapal/WT (break)	1.00116	1
Manapal/WT (red)	0.84297	0.216