Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07893	0.786
27DAP/17DAP	0.82332	0.523
39DAP/27DAP	1.07724	0.974
41DAP/39DAP	0.60997	0.06
42DAP/41DAP	1.08718	0.954
43DAP/42DAP	1.46381	0.195
47DAP/43DAP	1.11567	0.609
52DAP/47DAP	0.67889	0.158
57DAP/52DAP	0.72635	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16211	0.814
17DAP/reference	1.60367	0.306
27DAP/reference	2.81093	0.013
39DAP/reference	1.42754	0.413
41DAP/reference	1.06275	1
42DAP/reference	1.54925	0.001
43DAP/reference	1.77969	0.007
47DAP/reference	1.73591	0.001
52DAP/reference	0.96428	0.438
57DAP/reference	1.10088	0.291

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.70072	0.036
27DAP/17DAP	0.92579	0.648
39DAP/27DAP	0.65836	0.028
41DAP/39DAP	0.90486	0.68
42DAP/41DAP	1.07436	0.651
43DAP/42DAP	1.03683	0.446
47DAP/43DAP	0.92353	0.192
52DAP/47DAP	0.91586	0.426
57DAP/52DAP	0.79555	0.123
57DAP/7DAP	0.36892	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43996	0.042
17DAP/reference	1.27559	0.009
27DAP/reference	1.26341	0.01
39DAP/reference	1.46544	0.01
41DAP/reference	0.93084	0.247
42DAP/reference	1.12932	0.308
43DAP/reference	1.36821	0.011
47DAP/reference	1.19515	0.345
52DAP/reference	1.32796	0.036
57DAP/reference	1.41487	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77644	0.124
17DAP/reference	1.04166	0.999
27DAP/reference	1.51057	0.047
39DAP/reference	1.00403	0.509
41DAP/reference	1.03451	0.944
42DAP/reference	1.08164	0.744
43DAP/reference	0.65357	0.026
47DAP/reference	0.76953	0.032
52DAP/reference	0.51691	0.005
57DAP/reference	0.33439	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.72632	0.021
17DAP/reference	1.43785	0.162
27DAP/reference	2.10621	0.012
39DAP/reference	1.94442	0.005
41DAP/reference	1.47825	0.008
42DAP/reference	2.05352	0.009
43DAP/reference	2.85612	0.007
47DAP/reference	2.97908	0.006
52DAP/reference	1.7851	0.056
57DAP/reference	7.48516	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02182	1
26DAP/20DAP	0.98153	1
34DAP/26DAP	1.38941	0.819
51DAP/34DAP	0.55009	0.053
52DAP/51DAP	0.93883	1
53DAP/52DAP	0.69289	0.071
55DAP/53DAP	0.77728	0.04
57DAP/55DAP	1.00533	0.923
62DAP/57DAP	1.18822	0.767
68DAP/62DAP	0.93311	0.579
68DAP/14DAP	1.09111	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75385	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9641	0.692
Mature Green Tomato/Ripe Tomato	2.01661	0.025
Immature Eggplant/Mature Eggplant	0.58141	0.062
Ripe Pepper/Ripe Tomato	1.96145	1
Mature Eggplant/Ripe Tomato	1.60562	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37748	0.574
1-1-2/M82	1.37542	1
12-2/M82	0.88428	0.862
12-4/M82	1.25225	1
1-3/M82	1.81567	0.26
2-1-1/M82	0.83977	0.784
2-1/M82	0.82143	0.519
2-6/M82	1.49983	0.425
3-2/M82	0.8464	0.752
4-1-1/M82	1.42372	1
4-1/M82	1.4364	0.853
4-3-2/M82	1.56499	0.246
4-3/M82	1.07525	0.268
5-3/M82	1.00046	1
6-2/M82	1.27579	1
6-3/M82	0.97006	1
7-1/M82	0.99845	1
7-2/M82	1.63931	0.385
9-3-2/M82	2.10864	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96316
IL2-6/WTpooled	1.3836	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96321	1
IL12-4/WTpooled	1.04464	0.839
IL1-4/WTpooled	1.84112	1
WT/WTpooled	1.07711	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	0.89697	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85264	0.474
DC3000/delta hrp 6h	1.01399	0.95
DC3000/delta hrp 12h	1.13733	1
DC3000/delta hrp 24h	1.00278	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63172	0.023
DC3000 delta B/DC3000 delta AB	0.70015	0.024

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26509	1
Exp 36h	0.88289	0.82
Exp 60h	0.9349	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02466	1
Var 0h	0.5219	1
Var 12h I row2-row1	0.85515	0.338
Var 12h NI row2-row1	0.87837	0.494
Var 36h I row2-row1	0.9982	1
Var 36h NI row2-row1	1.29063	0.482
Var 60h I row2-row1	1.11327	0.523
Var 60h NI row2-row1	0.90305	1
Time course 0hI-0hNI	0.98011	0.9
Time course 12hI-12hNI	1.01923	0.774
Time course 36hI-36hNI	0.96921	0.194
Time course 60hI-60hNI	0.15735	0.005

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)	1.01717	0.921
transgenic ySAMdc/azygous control (breaker)	1.13242	0.248
transgenic ySAMdc/azygous control (red)	2.83447	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.6505	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32098	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.00249	0.307
Manapal/WT (break)	1.93372	0.381
Manapal/WT (red)	1.11715	0.222