Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16018	1
27DAP/17DAP	1.07939	1
39DAP/27DAP	1.04148	0.985
41DAP/39DAP	1.04501	0.742
42DAP/41DAP	0.82606	1
43DAP/42DAP	1.26541	1
47DAP/43DAP	0.91694	0.701
52DAP/47DAP	0.74103	0.461
57DAP/52DAP	0.89028	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92675	0.172
17DAP/reference	0.89747	0.031
27DAP/reference	0.92108	0.369
39DAP/reference	0.84785	0.064
41DAP/reference	0.84254	0.114
42DAP/reference	0.80496	0.003
43DAP/reference	0.83033	0.015
47DAP/reference	0.91167	0.137
52DAP/reference	0.94814	0.35
57DAP/reference	0.95713	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04964	0.99
27DAP/17DAP	0.8853	0.748
39DAP/27DAP	0.7948	0.141
41DAP/39DAP	1.20282	0.735
42DAP/41DAP	0.92335	0.503
43DAP/42DAP	0.78506	0.045
47DAP/43DAP	0.92307	0.696
52DAP/47DAP	1.13189	0.713
57DAP/52DAP	1.81065	0.087
57DAP/7DAP	1.1879	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99777	0.758
17DAP/reference	0.90192	0.167
27DAP/reference	1.08497	0.664
39DAP/reference	0.852	0.073
41DAP/reference	0.70647	0.02
42DAP/reference	0.70058	0.01
43DAP/reference	0.70606	0.022
47DAP/reference	0.81213	0.057
52DAP/reference	0.82231	0.09
57DAP/reference	0.68586	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00627	0.93
17DAP/reference	0.74322	0.005
27DAP/reference	0.87759	0.111
39DAP/reference	1.06438	0.529
41DAP/reference	0.83591	0.017
42DAP/reference	0.88042	0.019
43DAP/reference	0.75662	0.017
47DAP/reference	0.80143	0.012
52DAP/reference	0.83067	0.014
57DAP/reference	0.66608	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.016	1
17DAP/reference	0.86799	0.115
27DAP/reference	0.85916	0.043
39DAP/reference	0.86415	0.063
41DAP/reference	1.06686	0.674
42DAP/reference	0.95031	0.361
43DAP/reference	0.80553	0.029
47DAP/reference	0.7687	0.012
52DAP/reference	0.79549	0.164
57DAP/reference	1.06394	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9626	1
26DAP/20DAP	1.03911	1
34DAP/26DAP	0.89101	0.834
51DAP/34DAP	0.75818
52DAP/51DAP	1.38996	0.121
53DAP/52DAP	1.23962	0.444
55DAP/53DAP	1.08997	0.927
57DAP/55DAP	0.78653	0.222
62DAP/57DAP	1.17109	0.569
68DAP/62DAP	1.61567	0.145
68DAP/14DAP	1.30333	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68394	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.82958	0.063
Mature Green Tomato/Ripe Tomato	4.30691	0.015
Immature Eggplant/Mature Eggplant	0.35735	0.057
Ripe Pepper/Ripe Tomato	3.42894
Mature Eggplant/Ripe Tomato	0.49338	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.39812	0.877
1-1-2/M82	0.96876	1
12-2/M82	N/A	N/A
12-4/M82	0.93221	1
1-3/M82	0.98968
2-1-1/M82	0.68434
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.88362
4-1/M82	1.0222
4-3-2/M82	1.28382
4-3/M82	N/A	N/A
5-3/M82	1.88354
6-2/M82	0.64049
6-3/M82	1.09736	1
7-1/M82	N/A	N/A
7-2/M82	0.65871
9-3-2/M82	0.98868

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12579	1
IL2-6/WTpooled	1.39366	0.659
IL7-5/WTpooled	1.13754
IL7-3/WTpooled	1.10933	1
IL12-4/WTpooled	0.94377	1
IL1-4/WTpooled	1.04528	1
WT/WTpooled	1.06304	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	1.12406	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98851	1
DC3000/delta hrp 6h	1.07074	1
DC3000/delta hrp 12h	1.18501	1
DC3000/delta hrp 24h	0.69918	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9011	0.099
DC3000 delta B/DC3000 delta AB	1.10044	0.477

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	0.96746	1
Var 0h	1.06206	1
Var 12h I row2-row1	0.89891	0.565
Var 12h NI row2-row1	1.25995	0.649
Var 36h I row2-row1	0.81369	1
Var 36h NI row2-row1	1.36675	1
Var 60h I row2-row1	0.92028	0.582
Var 60h NI row2-row1	0.93168	0.977
Time course 0hI-0hNI	1.00675	1
Time course 12hI-12hNI	1.04938	0.724
Time course 36hI-36hNI	1.23733	0.028
Time course 60hI-60hNI	1.62116	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)	1.06885	0.431
transgenic ySAMdc/azygous control (breaker)	0.82305	0.49
transgenic ySAMdc/azygous control (red)	1.05217	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99422	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.53363	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49002	0.307
Manapal/WT (break)	0.65539	0.333
Manapal/WT (red)	0.54387	0.181