Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11752	0.838
27DAP/17DAP	1.07339	0.871
39DAP/27DAP	0.91173	0.594
41DAP/39DAP	1.2513	0.326
42DAP/41DAP	1.04263	1
43DAP/42DAP	0.88367	0.705
47DAP/43DAP	0.89228	0.64
52DAP/47DAP	1.48688	0.285
57DAP/52DAP	0.94561	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06527	0.96
17DAP/reference	0.94373	0.074
27DAP/reference	0.91691	0.187
39DAP/reference	0.99963	1
41DAP/reference	1.02285	0.759
42DAP/reference	0.9866	0.469
43DAP/reference	0.99875	0.942
47DAP/reference	0.98577	0.473
52DAP/reference	0.97511	0.283
57DAP/reference	0.9123	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96489	0.56
27DAP/17DAP	0.98089	0.782
39DAP/27DAP	1.05284	0.663
41DAP/39DAP	1.06748	0.883
42DAP/41DAP	1.06331	0.526
43DAP/42DAP	1.01359	1
47DAP/43DAP	1.01534	0.926
52DAP/47DAP	1.00136	1
57DAP/52DAP	1.02671	0.856
57DAP/7DAP	0.98318	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96471	0.326
17DAP/reference	0.98773	0.389
27DAP/reference	1.03455	0.131
39DAP/reference	1.04512	0.166
41DAP/reference	1.03031	0.577
42DAP/reference	1.10427	0.059
43DAP/reference	1.01797	0.569
47DAP/reference	0.9533	0.383
52DAP/reference	1.05589	0.212
57DAP/reference	1.00529	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14901	0.069
17DAP/reference	0.98643	0.673
27DAP/reference	0.92723	0.292
39DAP/reference	1.03516	0.705
41DAP/reference	1.07721	0.548
42DAP/reference	1.02253	0.899
43DAP/reference	1.1289	0.392
47DAP/reference	0.97669	0.284
52DAP/reference	0.9967	0.713
57DAP/reference	0.98609	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98974	0.526
17DAP/reference	0.99038	0.751
27DAP/reference	1.01838	0.51
39DAP/reference	0.93781	0.063
41DAP/reference	0.97046	0.185
42DAP/reference	1.02314	0.68
43DAP/reference	1.00722	0.961
47DAP/reference	0.91409	0.034
52DAP/reference	0.96144	0.538
57DAP/reference	0.87275	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03277	0.966
26DAP/20DAP	0.97843	1
34DAP/26DAP	0.95312	0.811
51DAP/34DAP	0.98534	0.873
52DAP/51DAP	1.06002	0.481
53DAP/52DAP	1.00822	0.921
55DAP/53DAP	0.96797	0.775
57DAP/55DAP	0.94696	0.76
62DAP/57DAP	0.86643	0.162
68DAP/62DAP	1.08599	0.89
68DAP/14DAP	0.9382	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96969	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89021
Mature Green Tomato/Ripe Tomato	0.85521	0.096
Immature Eggplant/Mature Eggplant	1.84395	0.051
Ripe Pepper/Ripe Tomato	0.84903	1
Mature Eggplant/Ripe Tomato	1.52944	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02233	1
1-1-2/M82	0.91428	1
12-2/M82	0.89084
12-4/M82	0.96229	1
1-3/M82	0.99362	1
2-1-1/M82	1.00088	1
2-1/M82	1.1456	1
2-6/M82	0.96746	1
3-2/M82	0.95037	0.752
4-1-1/M82	0.993	1
4-1/M82	0.89633	1
4-3-2/M82	1.00822	1
4-3/M82	0.90691	1
5-3/M82	0.99324	1
6-2/M82	1.05962	1
6-3/M82	1.03122	1
7-1/M82	0.94992	0.803
7-2/M82	1.01296	1
9-3-2/M82	0.86633	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.9957	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0795	1
IL12-4/WTpooled	1.06005	0.595
IL1-4/WTpooled	1.02931
WT/WTpooled	0.93214	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	1.7936	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05003	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.09389	1
DC3000/delta hrp 24h	1.05666	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04765	0.145
DC3000 delta B/DC3000 delta AB	1.02638	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.4116	1
Exp 36h	2.3716	0.693
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	0.96721	1
Var 0h	1.21726	0.374
Var 12h I row2-row1	1.31992	0.348
Var 12h NI row2-row1	1.03929	1
Var 36h I row2-row1	1.05872	1
Var 36h NI row2-row1	0.99195	0.852
Var 60h I row2-row1	1.03809	1
Var 60h NI row2-row1	1.00189	1
Time course 0hI-0hNI	1.04971	1
Time course 12hI-12hNI	1.02713	0.818
Time course 36hI-36hNI	1.09584	0.355
Time course 60hI-60hNI	1.22817	0.08

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)	1.39763	0.212
transgenic ySAMdc/azygous control (breaker)	0.88401	0.49
transgenic ySAMdc/azygous control (red)	1.89608	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97639	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58181	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72625	1
Manapal/WT (break)	0.71824	1
Manapal/WT (red)	0.517	0.199