Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05459	0.912
27DAP/17DAP	1.06462	0.916
39DAP/27DAP	2.09084	0.033
41DAP/39DAP	0.88655	0.54
42DAP/41DAP	1.29135	0.709
43DAP/42DAP	1.04682	0.937
47DAP/43DAP	1.09555	0.733
52DAP/47DAP	0.8471	0.609
57DAP/52DAP	1.43371	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89527	0.231
17DAP/reference	1.0169	0.843
27DAP/reference	1.15473	0.184
39DAP/reference	1.10091	0.377
41DAP/reference	1.02923	0.714
42DAP/reference	1.24382	0.001
43DAP/reference	1.30678	0.008
47DAP/reference	1.55183	0.001
52DAP/reference	1.3713	0.014
57DAP/reference	1.33549	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84846	0.121
27DAP/17DAP	1.30378	0.094
39DAP/27DAP	1.14411	0.383
41DAP/39DAP	0.95602	0.839
42DAP/41DAP	1.26751	0.134
43DAP/42DAP	1.15779	0.112
47DAP/43DAP	1.12708	0.396
52DAP/47DAP	1.0336	0.927
57DAP/52DAP	1.20295	0.358
57DAP/7DAP	1.65977	0.153

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08595	0.534
17DAP/reference	1.0025	1
27DAP/reference	1.15697	0.01
39DAP/reference	1.09785	0.282
41DAP/reference	1.02791	0.848
42DAP/reference	1.15822	0.018
43DAP/reference	1.3507	0.007
47DAP/reference	1.29496	0.051
52DAP/reference	1.08044	0.563
57DAP/reference	1.12107	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82589	0.038
17DAP/reference	0.94687	0.253
27DAP/reference	1.12952	0.292
39DAP/reference	0.98814	0.539
41DAP/reference	0.85836	0.058
42DAP/reference	0.98944	0.534
43DAP/reference	0.93961	0.438
47DAP/reference	1.15635	0.153
52DAP/reference	0.71522	0.004
57DAP/reference	0.70827	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97216	0.607
17DAP/reference	0.88607	0.364
27DAP/reference	1.09685	0.207
39DAP/reference	1.18066	0.1
41DAP/reference	0.96382	0.107
42DAP/reference	1.28644	0.072
43DAP/reference	1.37796	0.013
47DAP/reference	1.30025	0.011
52DAP/reference	1.64884	0.03
57DAP/reference	1.72736	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92303	1
26DAP/20DAP	1.40976	0.308
34DAP/26DAP	0.9119	0.712
51DAP/34DAP	1.30081	0.108
52DAP/51DAP	0.73152	1
53DAP/52DAP	1.28506	0.095
55DAP/53DAP	0.81191	0.037
57DAP/55DAP	1.26491	0.242
62DAP/57DAP	0.58059	0.28
68DAP/62DAP	1.34385	0.831
68DAP/14DAP	1.03836	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97211	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93617	0.605
Mature Green Tomato/Ripe Tomato	0.60575	0.06
Immature Eggplant/Mature Eggplant	1.22481	0.074
Ripe Pepper/Ripe Tomato	0.85457	1
Mature Eggplant/Ripe Tomato	0.59702	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10245	1
1-1-2/M82	1.22027
12-2/M82	1.02014	1
12-4/M82	1.02038	1
1-3/M82	2.07345	0.255
2-1-1/M82	1.08328	0.689
2-1/M82	0.89382	0.74
2-6/M82	0.94581	1
3-2/M82	0.96009
4-1-1/M82	1.09176	1
4-1/M82	0.90186
4-3-2/M82	1.26742
4-3/M82	1.26459	1
5-3/M82	0.95342	1
6-2/M82	1.26953	1
6-3/M82	0.99066	1
7-1/M82	0.94766
7-2/M82	1.2716	0.299
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	1.18801	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8585	0.31
IL12-4/WTpooled	1.2012	0.624
IL1-4/WTpooled	0.80733	0.562
WT/WTpooled	1.06672	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	1.14643	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9773	1
DC3000/delta hrp 6h	1.12093	1
DC3000/delta hrp 12h	1.02864	1
DC3000/delta hrp 24h	0.93916	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08653	0.384
DC3000 delta B/DC3000 delta AB	1.31204	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16517	1
Exp 36h	0.99214	1
Exp 60h	1.18045	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01991	1
Var 0h	0.55049	0.936
Var 12h I row2-row1	1.09063	0.654
Var 12h NI row2-row1	1.08053	0.649
Var 36h I row2-row1	1.33794	0.489
Var 36h NI row2-row1	1.04829	1
Var 60h I row2-row1	0.80189	0.439
Var 60h NI row2-row1	0.82298	0.572
Time course 0hI-0hNI	0.98312	0.955
Time course 12hI-12hNI	0.95935	0.698
Time course 36hI-36hNI	1.03915	0.799
Time course 60hI-60hNI	1.17906	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)	1.00089	1
transgenic ySAMdc/azygous control (breaker)	0.70955	0.125
transgenic ySAMdc/azygous control (red)	0.94339	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20233	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88617	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79493	1
Manapal/WT (break)	0.93659	1
Manapal/WT (red)	0.71098	0.181