Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83568	0.419
27DAP/17DAP	1.10963	0.859
39DAP/27DAP	1.02977	1
41DAP/39DAP	1.0721	0.797
42DAP/41DAP	1.77223	0.026
43DAP/42DAP	1.2418	0.906
47DAP/43DAP	2.97188	0.172
52DAP/47DAP	0.58906	0.071
57DAP/52DAP	1.58989	0.508

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9188	0.269
17DAP/reference	1.071	0.369
27DAP/reference	1.06814	0.216
39DAP/reference	1.0501	0.465
41DAP/reference	1.01296	0.814
42DAP/reference	0.90585	0.043
43DAP/reference	1.05598	0.518
47DAP/reference	0.93446	0.345
52DAP/reference	1.05041	0.607
57DAP/reference	1.05157	0.621

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1285	0.422
27DAP/17DAP	1.17141	0.505
39DAP/27DAP	1.52025	0.112
41DAP/39DAP	0.53426	0.066
42DAP/41DAP	1.65172	0.004
43DAP/42DAP	2.14958	0.014
47DAP/43DAP	1.02921	0.897
52DAP/47DAP	1.64245	0.074
57DAP/52DAP	0.60686	0.059
57DAP/7DAP	0.98211

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92621	0.157
17DAP/reference	0.79596	0.049
27DAP/reference	0.80288	0.015
39DAP/reference	0.73967	0.012
41DAP/reference	0.7329	0.026
42DAP/reference	0.7131	0.012
43DAP/reference	0.66273	0.016
47DAP/reference	0.90403	0.383
52DAP/reference	0.65189	0.015
57DAP/reference	0.72722	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06395	0.724
17DAP/reference	1.08115	0.644
27DAP/reference	0.95728	0.423
39DAP/reference	1.02321	0.956
41DAP/reference	0.96116	0.373
42DAP/reference	0.87335	0.098
43DAP/reference	0.9645	0.516
47DAP/reference	0.98936	0.609
52DAP/reference	1.16148	0.03
57DAP/reference	1.19733	0.036

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92566	0.311
17DAP/reference	0.91328	0.381
27DAP/reference	0.72874	0.033
39DAP/reference	0.74936	0.021
41DAP/reference	0.74457	0.031
42DAP/reference	0.98518	0.816
43DAP/reference	0.98294	0.614
47DAP/reference	0.89141	0.207
52DAP/reference	1.27241	0.357
57DAP/reference	0.75474	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.78883	0.807
26DAP/20DAP	1.11002
34DAP/26DAP	4.93432	0.819
51DAP/34DAP	1.55706	0.473
52DAP/51DAP	1.25122	0.176
53DAP/52DAP	1.29097	0.882
55DAP/53DAP	1.31735	0.741
57DAP/55DAP	1.22878	0.249
62DAP/57DAP	1.02353	1
68DAP/62DAP	0.78831	0.177
68DAP/14DAP	0.79129	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.0284	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.82005	0.058
Mature Green Tomato/Ripe Tomato	0.1258	0.017
Immature Eggplant/Mature Eggplant	0.41729
Ripe Pepper/Ripe Tomato	0.54459	1
Mature Eggplant/Ripe Tomato	0.3152	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92964	0.944
1-1-2/M82	N/A	N/A
12-2/M82	0.95106	0.661
12-4/M82	1.2843	1
1-3/M82	1.9606	0.248
2-1-1/M82	0.90154	0.683
2-1/M82	1.02598	1
2-6/M82	1.05258	0.695
3-2/M82	1.05016	0.717
4-1-1/M82	1.39146	1
4-1/M82	0.89545
4-3-2/M82	1.31967
4-3/M82	0.93652	1
5-3/M82	0.94742	1
6-2/M82	1.00081	1
6-3/M82	1.07885
7-1/M82	0.83889	0.803
7-2/M82	1.11466	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06573	1
IL2-6/WTpooled	1.05685	0.456
IL7-5/WTpooled	0.94662	1
IL7-3/WTpooled	0.92365	0.418
IL12-4/WTpooled	0.87797	0.71
IL1-4/WTpooled	0.97471	0.834
WT/WTpooled	0.93289	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.95603	0.95
DC3000/delta hrp 12h	0.98274	1
DC3000/delta hrp 24h	N/A	N/A

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	0.83478	1
Exp 36h	0.88012	0.406
Exp 60h	0.86813	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1244	1
Var 0h	1.01454	1
Var 12h I row2-row1	0.93818	0.948
Var 12h NI row2-row1	1.78704
Var 36h I row2-row1	1.11781	0.908
Var 36h NI row2-row1	1.20202
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.60066	1
Time course 0hI-0hNI	0.87917	0.852
Time course 12hI-12hNI	1.06253	0.88
Time course 36hI-36hNI	1.57188	0.07
Time course 60hI-60hNI	2.16767	0.16

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)	0.98605	0.789
transgenic ySAMdc/azygous control (breaker)	0.51185	0.131
transgenic ySAMdc/azygous control (red)	1.05735	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97331	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77135	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97986	1
Manapal/WT (break)	0.81651	1
Manapal/WT (red)	0.91874	0.503