Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95	0.617
27DAP/17DAP	1.08433	0.89
39DAP/27DAP	0.88308	0.641
41DAP/39DAP	1.59077	0.289
42DAP/41DAP	0.725	1
43DAP/42DAP	1.18118	1
47DAP/43DAP	1.1987	0.889
52DAP/47DAP	1.39045	0.654
57DAP/52DAP	0.9437	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94335	0.284
17DAP/reference	1.03914	0.201
27DAP/reference	0.99845	0.923
39DAP/reference	0.94733	0.24
41DAP/reference	0.84394	0.201
42DAP/reference	0.79031	0.018
43DAP/reference	0.72867	0.058
47DAP/reference	1.21586	0.419
52DAP/reference	0.86776	0.35
57DAP/reference	0.69747	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95276	0.56
27DAP/17DAP	0.97709	0.854
39DAP/27DAP	1.04123	0.587
41DAP/39DAP	0.94748	0.804
42DAP/41DAP	1.04913	0.783
43DAP/42DAP	1.13511	0.094
47DAP/43DAP	1.00641	0.973
52DAP/47DAP	0.98898	0.93
57DAP/52DAP	0.97325	0.628
57DAP/7DAP	1.00863	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96948	0.445
17DAP/reference	0.92982	0.108
27DAP/reference	0.78998	0.01
39DAP/reference	0.88028	0.043
41DAP/reference	0.83351	0.094
42DAP/reference	0.83353	0.02
43DAP/reference	0.89256	0.061
47DAP/reference	1.06414	0.493
52DAP/reference	1.09089	0.428
57DAP/reference	1.01315	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97573	0.655
17DAP/reference	0.92063	0.12
27DAP/reference	0.90498	0.167
39DAP/reference	0.88333	0.081
41DAP/reference	0.92629	0.127
42DAP/reference	0.88041	0.089
43DAP/reference	0.90864	0.17
47DAP/reference	0.90043	0.025
52DAP/reference	0.9612	0.239
57DAP/reference	0.85695	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85971	0.047
17DAP/reference	0.9423	0.281
27DAP/reference	0.91212	0.085
39DAP/reference	0.81964	0.007
41DAP/reference	0.94544	0.371
42DAP/reference	0.89527	0.22
43DAP/reference	1.07205	0.432
47DAP/reference	1.13988	0.019
52DAP/reference	0.92139	0.444
57DAP/reference	0.93508	0.258

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03631	0.966
26DAP/20DAP	0.90781	0.512
34DAP/26DAP	1.02938	1
51DAP/34DAP	1.3854	0.052
52DAP/51DAP	0.83956	0.079
53DAP/52DAP	0.96539	0.811
55DAP/53DAP	0.83859	0.169
57DAP/55DAP	0.98732	0.875
62DAP/57DAP	1.11045	0.445
68DAP/62DAP	1.26283	0.166
68DAP/14DAP	1.27743	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79708	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.35338	0.077
Mature Green Tomato/Ripe Tomato	0.56355	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.18602	1
Mature Eggplant/Ripe Tomato	0.17648	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00111	1
1-1-2/M82	1.0743	1
12-2/M82	0.97343	1
12-4/M82	1.02793	1
1-3/M82	0.92181	0.378
2-1-1/M82	1.06992	1
2-1/M82	1.02095	1
2-6/M82	1.02345	1
3-2/M82	1.05278	0.967
4-1-1/M82	1.1261	1
4-1/M82	1.17075	0.363
4-3-2/M82	1.24888	0.262
4-3/M82	1.59796	1
5-3/M82	0.82132	0.642
6-2/M82	0.69154	1
6-3/M82	1.10009	1
7-1/M82	0.96194	1
7-2/M82	0.98241	1
9-3-2/M82	1.18459	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85456
IL2-6/WTpooled	0.88101	0.383
IL7-5/WTpooled	2.76484
IL7-3/WTpooled	0.88201	0.31
IL12-4/WTpooled	1.16236	0.839
IL1-4/WTpooled	0.90511	0.562
WT/WTpooled	1.0207	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	2.99486	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01532	0.921
DC3000/delta hrp 6h	0.67112	0.801
DC3000/delta hrp 12h	0.90239	1
DC3000/delta hrp 24h	1.36785	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06754	0.121
DC3000 delta B/DC3000 delta AB	1.06667	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95684	1
Exp 36h	0.849	0.699
Exp 60h	0.96846	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99351	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.07246	0.216
Var 12h NI row2-row1	1.02356	1
Var 36h I row2-row1	1.1392	1
Var 36h NI row2-row1	0.94848	0.791
Var 60h I row2-row1	1.5067	0.562
Var 60h NI row2-row1	1.28961	0.904
Time course 0hI-0hNI	1.03718	0.764
Time course 12hI-12hNI	1.00775	1
Time course 36hI-36hNI	0.98536	0.514
Time course 60hI-60hNI	1.16094	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)	0.78349	0.213
transgenic ySAMdc/azygous control (breaker)	1.19431	0.248
transgenic ySAMdc/azygous control (red)	1.00611	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03051	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05827	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93689	1
Manapal/WT (break)	1.27759	0.381
Manapal/WT (red)	0.58425	0.181