Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95093	0.683
27DAP/17DAP	1.18271	0.845
39DAP/27DAP	1.04989	1
41DAP/39DAP	1.10417	0.663
42DAP/41DAP	1.59215	0.14
43DAP/42DAP	1.19583	0.985
47DAP/43DAP	0.6798	0.175
52DAP/47DAP	1.47726	0.521
57DAP/52DAP	0.96293	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98299	0.601
17DAP/reference	1.05377	0.492
27DAP/reference	0.93923	0.428
39DAP/reference	1.00934	1
41DAP/reference	1.0066	1
42DAP/reference	0.8288	0.011
43DAP/reference	1.02089	0.928
47DAP/reference	0.85811	0.009
52DAP/reference	0.90137	0.152
57DAP/reference	0.91919	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01973	1
27DAP/17DAP	1.17121	0.476
39DAP/27DAP	1.23157	0.422
41DAP/39DAP	1.22244	0.753
42DAP/41DAP	1.04422	1
43DAP/42DAP	1.16175	0.413
47DAP/43DAP	0.9939	0.985
52DAP/47DAP	0.8993	0.677
57DAP/52DAP	1.00989	0.929
57DAP/7DAP	1.21702	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97389	0.613
17DAP/reference	0.93162	0.192
27DAP/reference	0.99204	0.614
39DAP/reference	0.80935	0.017
41DAP/reference	0.77352	0.098
42DAP/reference	0.88063	0.095
43DAP/reference	0.84902	0.082
47DAP/reference	0.85897	0.079
52DAP/reference	0.73656	0.028
57DAP/reference	0.88165	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08106	0.559
17DAP/reference	1.00572	0.659
27DAP/reference	0.9052	0.249
39DAP/reference	0.98699	0.539
41DAP/reference	0.83219	0.133
42DAP/reference	0.87322	0.067
43DAP/reference	1.14182	0.368
47DAP/reference	0.91734	0.149
52DAP/reference	0.79078	0.006
57DAP/reference	1.15864	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96629	0.422
17DAP/reference	1.07261	0.738
27DAP/reference	1.10736	0.531
39DAP/reference	1.20162	0.091
41DAP/reference	0.92501	0.293
42DAP/reference	0.83319	0.032
43DAP/reference	0.794	0.03
47DAP/reference	0.95885	0.421
52DAP/reference	0.98864	0.838
57DAP/reference	0.70681	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90261	0.961
26DAP/20DAP	0.77399	0.512
34DAP/26DAP	1.42573	1
51DAP/34DAP	1.32863	0.814
52DAP/51DAP	1.6811	0.246
53DAP/52DAP	1.01638	0.983
55DAP/53DAP	1.12336	1
57DAP/55DAP	1.00957	0.867
62DAP/57DAP	0.98373	1
68DAP/62DAP	1.3809	0.8
68DAP/14DAP	0.50692

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93785	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.3406

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.79453
1-1-2/M82	0.75926
12-2/M82	N/A	N/A
12-4/M82	1.02183	1
1-3/M82	0.60749
2-1-1/M82	1.43258
2-1/M82	N/A	N/A
2-6/M82	1.13508	0.505
3-2/M82	0.86899
4-1-1/M82	1.07624
4-1/M82	1.70295
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.90303	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	0.98593	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03802	1
IL12-4/WTpooled	0.93258	1
IL1-4/WTpooled	1.01147	1
WT/WTpooled	1.00578	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	0.93173	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12858	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.92744	1
DC3000/delta hrp 24h	1.14108	0.397

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	0.89685	1
Var 0h	0.66299	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.95636	0.906
Var 36h I row2-row1	1.49725	0.908
Var 36h NI row2-row1	1.42812
Var 60h I row2-row1	0.92841
Var 60h NI row2-row1	1.09663	0.904
Time course 0hI-0hNI	0.91294	0.468
Time course 12hI-12hNI	1.23674	0.544
Time course 36hI-36hNI	0.99453	0.708
Time course 60hI-60hNI	0.87248	0.646

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)	1.91616	0.384
transgenic ySAMdc/azygous control (breaker)	1.65521	1
transgenic ySAMdc/azygous control (red)	1.00008	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94479	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98751	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09682	1
Manapal/WT (break)	1.69527	0.14
Manapal/WT (red)	0.82603	0.181