Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81147	0.297
27DAP/17DAP	0.95175	0.939
39DAP/27DAP	1.17764	0.59
41DAP/39DAP	0.81622	0.311
42DAP/41DAP	1.23373	0.702
43DAP/42DAP	1.44267	0.226
47DAP/43DAP	1.56822	0.215
52DAP/47DAP	1.14747	0.844
57DAP/52DAP	0.92894	0.857

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0245	0.96
17DAP/reference	0.98675	0.737
27DAP/reference	1.10824	0.314
39DAP/reference	0.98398	0.816
41DAP/reference	0.94866	0.542
42DAP/reference	1.2205	0.058
43DAP/reference	0.9932	0.82
47DAP/reference	0.9661	0.345
52DAP/reference	1.04685	0.766
57DAP/reference	1.07265	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78489	0.131
27DAP/17DAP	1.3585	0.134
39DAP/27DAP	0.90178	0.45
41DAP/39DAP	0.93196	0.822
42DAP/41DAP	0.9194	0.436
43DAP/42DAP	1.24914	0.066
47DAP/43DAP	1.20089	0.08
52DAP/47DAP	1.04314	0.927
57DAP/52DAP	0.99639	0.862
57DAP/7DAP	0.98099	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02227	1
17DAP/reference	1.07665	0.269
27DAP/reference	1.0412	0.453
39DAP/reference	1.09528	0.077
41DAP/reference	1.09971	0.27
42DAP/reference	1.14165	0.009
43DAP/reference	1.13811	0.124
47DAP/reference	1.05811	0.67
52DAP/reference	1.07224	0.401
57DAP/reference	1.00843	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12585	0.41
17DAP/reference	1.42698	0.008
27DAP/reference	1.2378	0.249
39DAP/reference	1.34741	0.034
41DAP/reference	1.37175	0.094
42DAP/reference	1.36803	0.094
43DAP/reference	1.16831	0.441
47DAP/reference	1.08757	0.143
52DAP/reference	1.21033	0.053
57DAP/reference	1.14463	0.244

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11171	0.076
17DAP/reference	1.11293	0.371
27DAP/reference	1.02705	0.695
39DAP/reference	0.99113	0.693
41DAP/reference	1.15255	0.089
42DAP/reference	0.9711	0.552
43DAP/reference	1.07088	0.474
47DAP/reference	1.02962	1
52DAP/reference	0.88977	0.415
57DAP/reference	1.21037	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94643	1
26DAP/20DAP	1.17712	0.604
34DAP/26DAP	1.08133	1
51DAP/34DAP	0.94132	0.737
52DAP/51DAP	0.77301	1
53DAP/52DAP	1.01659	1
55DAP/53DAP	0.9255	0.698
57DAP/55DAP	1.0505	0.915
62DAP/57DAP	0.77517	0.088
68DAP/62DAP	1.17483	0.944
68DAP/14DAP	1.10303	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.007	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74296	0.295
Mature Green Tomato/Ripe Tomato	0.63731	0.06
Immature Eggplant/Mature Eggplant	1.24779	0.174
Ripe Pepper/Ripe Tomato	0.71928	0.293
Mature Eggplant/Ripe Tomato	0.70915	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21761
1-1-2/M82	0.85365
12-2/M82	1.10851
12-4/M82	1.14978	1
1-3/M82	0.87219
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.05347
3-2/M82	1.21958	0.717
4-1-1/M82	1.18835	1
4-1/M82	1.60961	0.225
4-3-2/M82	1.39198
4-3/M82	0.82259	0.72
5-3/M82	1.09893	1
6-2/M82	1.15136
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.09892
9-3-2/M82	1.59137	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05865
IL2-6/WTpooled	1.40779
IL7-5/WTpooled	0.85581
IL7-3/WTpooled	0.9998	1
IL12-4/WTpooled	1.13503	1
IL1-4/WTpooled	1.02429	1
WT/WTpooled	1.01013	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	0.94714	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0438	0.914
DC3000/delta hrp 6h	0.82685	0.95
DC3000/delta hrp 12h	1.28225	1
DC3000/delta hrp 24h	0.94447	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54515
DC3000 delta B/DC3000 delta AB	0.66984	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0281	1
Exp 36h	0.99583	1
Exp 60h	1.15785	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00078	1
Var 0h	1.05451	0.98
Var 12h I row2-row1	0.79586	0.353
Var 12h NI row2-row1	0.91285	0.82
Var 36h I row2-row1	0.90183	1
Var 36h NI row2-row1	1.07839	1
Var 60h I row2-row1	1.29998	1
Var 60h NI row2-row1	1.02454	1
Time course 0hI-0hNI	0.92657	0.446
Time course 12hI-12hNI	0.95567	0.575
Time course 36hI-36hNI	0.82714	0.055
Time course 60hI-60hNI	0.33685	0.005

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)	1.05086	0.431
transgenic ySAMdc/azygous control (breaker)	0.87929	0.49
transgenic ySAMdc/azygous control (red)	0.95922	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97635	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86483	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0588	1
Manapal/WT (break)	1.06583	1
Manapal/WT (red)	1.3006	0.142