Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21017	0.523
27DAP/17DAP	1.23985	0.859
39DAP/27DAP	1.21223	0.894
41DAP/39DAP	0.99503	0.802
42DAP/41DAP	1.23568	0.871
43DAP/42DAP	1.08166	1
47DAP/43DAP	0.97784	0.884
52DAP/47DAP	0.77034	0.391
57DAP/52DAP	1.11861	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97938	0.513
17DAP/reference	0.96925	0.474
27DAP/reference	1.0225	0.66
39DAP/reference	1.02106	0.581
41DAP/reference	1.02917	0.667
42DAP/reference	0.95888	0.124
43DAP/reference	0.97593	0.555
47DAP/reference	0.99134	0.535
52DAP/reference	0.9989	0.749
57DAP/reference	1.12008	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01096	0.961
27DAP/17DAP	1.01827	0.951
39DAP/27DAP	0.99302	1
41DAP/39DAP	0.96622	0.923
42DAP/41DAP	1.00029	0.936
43DAP/42DAP	1.01383	0.513
47DAP/43DAP	1.02831	0.772
52DAP/47DAP	0.96225	0.677
57DAP/52DAP	0.97697	0.601
57DAP/7DAP	0.98927	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.07694	0.027
17DAP/reference	3.2461	0.006
27DAP/reference	2.57416	0.007
39DAP/reference	2.95251	0.005
41DAP/reference	3.01934	0.011
42DAP/reference	3.8432	0.006
43DAP/reference	3.70949	0.007
47DAP/reference	2.20012	0.173
52DAP/reference	2.65899	0.007
57DAP/reference	2.4213	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98522	0.786
17DAP/reference	0.94141	0.143
27DAP/reference	0.92286	0.173
39DAP/reference	0.91108	0.122
41DAP/reference	0.97012	0.412
42DAP/reference	1.00575	1
43DAP/reference	0.96045	0.516
47DAP/reference	1.02972	0.212
52DAP/reference	0.93266	0.016
57DAP/reference	0.94017	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19542	0.026
17DAP/reference	1.58949	0.376
27DAP/reference	3.71721	0.018
39DAP/reference	3.73946	0.006
41DAP/reference	2.57856	0.009
42DAP/reference	2.94799	0.014
43DAP/reference	2.69935	0.032
47DAP/reference	0.96151	0.278
52DAP/reference	4.16234	0.034
57DAP/reference	1.70838	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07849	0.966
26DAP/20DAP	1.01388	1
34DAP/26DAP	1.01129	1
51DAP/34DAP	1.04389	0.597
52DAP/51DAP	0.99963	1
53DAP/52DAP	1.09776	0.623
55DAP/53DAP	0.97776	0.746
57DAP/55DAP	0.97359	0.902
62DAP/57DAP	0.899	0.466
68DAP/62DAP	0.87117	0.543
68DAP/14DAP	1.22559	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88714	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18643	0.417
Mature Green Tomato/Ripe Tomato	0.94539	0.611
Immature Eggplant/Mature Eggplant	1.13846	0.321
Ripe Pepper/Ripe Tomato	0.9551	1
Mature Eggplant/Ripe Tomato	0.68471	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97017	0.961
1-1-2/M82	0.98426	1
12-2/M82	0.94807	0.955
12-4/M82	0.99803	1
1-3/M82	0.93107	0.378
2-1-1/M82	0.98375	1
2-1/M82	0.90723	0.74
2-6/M82	0.94063	1
3-2/M82	0.95902
4-1-1/M82	0.9532	1
4-1/M82	1.02309	1
4-3-2/M82	0.79822	0.487
4-3/M82	0.91019	0.72
5-3/M82	0.96691	1
6-2/M82	0.94103	1
6-3/M82	1.05092	1
7-1/M82	0.94524	1
7-2/M82	0.93459	0.881
9-3-2/M82	0.91801	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.7734
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08592	1
IL12-4/WTpooled	0.97797	1
IL1-4/WTpooled	1.0149	1
WT/WTpooled	0.98514	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	0.81864	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01337	0.921
DC3000/delta hrp 6h	0.94764	0.95
DC3000/delta hrp 12h	1.02605	1
DC3000/delta hrp 24h	1.04059	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2459	0.076
DC3000 delta B/DC3000 delta AB	1.13541	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96485	1
Exp 36h	0.8981	0.749
Exp 60h	0.81028	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01801	1
Var 0h	1.33781	0.169
Var 12h I row2-row1	1.13144	0.204
Var 12h NI row2-row1	1.0296	1
Var 36h I row2-row1	1.01182	1
Var 36h NI row2-row1	0.91418	0.478
Var 60h I row2-row1	0.95781	0.439
Var 60h NI row2-row1	1.0967	0.904
Time course 0hI-0hNI	1.06293	0.833
Time course 12hI-12hNI	1.06555	0.633
Time course 36hI-36hNI	1.04703	0.248
Time course 60hI-60hNI	1.50198	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)	0.90852	0.315
transgenic ySAMdc/azygous control (breaker)	1.14781	0.248
transgenic ySAMdc/azygous control (red)	1.11285	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96979	0.153

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26693	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.82224	0.096
Manapal/WT (break)	1.94398	0.183
Manapal/WT (red)	1.58164	0.137