Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82591	0.265
27DAP/17DAP	1.08518	1
39DAP/27DAP	1.05231	0.906
41DAP/39DAP	1.05951	0.833
42DAP/41DAP	1.03814	1
43DAP/42DAP	0.83479	0.71
47DAP/43DAP	1.69148	0.201
52DAP/47DAP	2.22	0.119
57DAP/52DAP	0.98266	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01975	0.611
17DAP/reference	0.93466	0.12
27DAP/reference	0.96689	0.525
39DAP/reference	1.18502	0.027
41DAP/reference	1.07776	0.187
42DAP/reference	0.92452	0.075
43DAP/reference	0.96909	0.611
47DAP/reference	0.94705	0.09
52DAP/reference	1.00309	0.73
57DAP/reference	1.25058	0.057

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22691	0.728
27DAP/17DAP	0.97517	0.919
39DAP/27DAP	0.65453	0.036
41DAP/39DAP	1.1002	0.682
42DAP/41DAP	1.03702	0.961
43DAP/42DAP	1.04397	0.83
47DAP/43DAP	1.04902	1
52DAP/47DAP	1.66932	0.203
57DAP/52DAP	1.44372	0.225
57DAP/7DAP	2.12009	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87957	0.168
17DAP/reference	1.00413	0.693
27DAP/reference	1.1439	0.035
39DAP/reference	1.21119	0.086
41DAP/reference	1.1549	0.363
42DAP/reference	1.56491	0.016
43DAP/reference	1.12415	0.408
47DAP/reference	1.00038	1
52DAP/reference	1.10918	0.197
57DAP/reference	1.06971	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16293	0.531
17DAP/reference	1.13408	0.348
27DAP/reference	1.0709	0.607
39DAP/reference	0.97174	0.359
41DAP/reference	1.12653	0.293
42DAP/reference	1.10442	0.274
43DAP/reference	1.34317	0.259
47DAP/reference	1.00547	1
52DAP/reference	0.96905	0.407
57DAP/reference	0.94011	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99073	0.699
17DAP/reference	1.12401	0.657
27DAP/reference	1.33321	0.056
39DAP/reference	1.39537	0.012
41DAP/reference	1.08052	0.439
42DAP/reference	0.97912	0.816
43DAP/reference	0.86077	0.158
47DAP/reference	0.85844	0.043
52DAP/reference	0.95245	0.582
57DAP/reference	1.01731	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.92754	0.966
26DAP/20DAP	0.58079	0.223
34DAP/26DAP	0.81612
51DAP/34DAP	0.98995	0.77
52DAP/51DAP	1.57747	0.51
53DAP/52DAP	0.93071	0.741
55DAP/53DAP	0.84291	0.5
57DAP/55DAP	1.22798	0.955
62DAP/57DAP	1.1583	0.8
68DAP/62DAP	1.00985	0.834
68DAP/14DAP	1.12943	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49859	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.64423	0.058
Mature Green Tomato/Ripe Tomato	0.17867	0.019
Immature Eggplant/Mature Eggplant	1.65553	0.05
Ripe Pepper/Ripe Tomato	0.18233	0.293
Mature Eggplant/Ripe Tomato	0.80735	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37787
1-1-2/M82	0.92263
12-2/M82	N/A	N/A
12-4/M82	0.59447
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.6674
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.9353
5-3/M82	1.04346	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.89819
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08596	1
IL2-6/WTpooled	0.9294	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.2346	0.362
IL12-4/WTpooled	0.78148	0.71
IL1-4/WTpooled	1.11733	1
WT/WTpooled	0.99503	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	1.39249	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93996	1
DC3000/delta hrp 6h	1.20589	0.609
DC3000/delta hrp 12h	0.76142
DC3000/delta hrp 24h	1.23589	0.123

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	0.90554

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07788	1
Exp 36h	0.95158	0.879
Exp 60h	0.95149	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.84116
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.00423	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.88656	0.615
Time course 12hI-12hNI	1.0687	0.687
Time course 36hI-36hNI	1.10014	0.218
Time course 60hI-60hNI	0.62641	0.006

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)	1.11834	0.36
transgenic ySAMdc/azygous control (breaker)	0.55597	0.119
transgenic ySAMdc/azygous control (red)	0.94934	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28633	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62384	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.25352	0.096
Manapal/WT (break)	1.32002	0.14
Manapal/WT (red)	1.24577	0.413