Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27429	0.188
27DAP/17DAP	1.06661	0.922
39DAP/27DAP	1.1626	0.825
41DAP/39DAP	1.01197	0.992
42DAP/41DAP	1.17862	0.843
43DAP/42DAP	1.10892	0.999
47DAP/43DAP	0.96502	0.768
52DAP/47DAP	1.04339	0.942
57DAP/52DAP	1.2939	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77982	0.049
17DAP/reference	1.16751	0.631
27DAP/reference	2.34271	0.075
39DAP/reference	1.54149	0.393
41DAP/reference	1.63074	0.043
42DAP/reference	0.9495	0.531
43DAP/reference	1.78533
47DAP/reference	0.97409	0.418
52DAP/reference	1.77538	0.008
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87707	0.509
27DAP/17DAP	0.94043	0.724
39DAP/27DAP	0.89997	0.45
41DAP/39DAP	0.89131	0.412
42DAP/41DAP	0.95718	0.7
43DAP/42DAP	0.95441	0.538
47DAP/43DAP	1.00361	0.99
52DAP/47DAP	1.22724	0.424
57DAP/52DAP	1.09723	0.596
57DAP/7DAP	1.2162	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13078	0.613
17DAP/reference	0.8663	0.124
27DAP/reference	0.9619	0.348
39DAP/reference	0.94972	0.354
41DAP/reference	1.05317	0.811
42DAP/reference	0.9015	0.082
43DAP/reference	0.81461	0.042
47DAP/reference	1.54707	0.421
52DAP/reference	0.77097	0.053
57DAP/reference	0.78709	0.047

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96334	0.38
17DAP/reference	1.81704	0.147
27DAP/reference	0.98964	0.642
39DAP/reference	1.67592	0.128
41DAP/reference	1.93095	0.023
42DAP/reference	2.48632	0.007
43DAP/reference	1.1525	0.569
47DAP/reference	1.56408	0.026
52DAP/reference	1.12065	0.168
57DAP/reference	1.16096	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78656	0.074
17DAP/reference	1.21926	0.456
27DAP/reference	1.35197	0.644
39DAP/reference	0.92156	0.147
41DAP/reference	1.00536	1
42DAP/reference	1.37584	0.364
43DAP/reference	3.08791	0.175
47DAP/reference	1.54439	0.251
52DAP/reference	0.93355	0.538
57DAP/reference	2.11464	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.4375	0.966
26DAP/20DAP	0.99842	1
34DAP/26DAP	0.74276	0.841
51DAP/34DAP	1.05798	0.978
52DAP/51DAP	2.08557	0.039
53DAP/52DAP	0.90617	0.435
55DAP/53DAP	1.42616	0.061
57DAP/55DAP	0.68365	0.145
62DAP/57DAP	0.68355	0.871
68DAP/62DAP	0.75312	0.543
68DAP/14DAP	0.68036	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79296	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00644
Mature Green Tomato/Ripe Tomato	2.5574	0.044
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.17981
Mature Eggplant/Ripe Tomato	0.54762	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.58026
12-2/M82	N/A	N/A
12-4/M82	0.70334	0.274
1-3/M82	1.13198
2-1-1/M82	0.99499	1
2-1/M82	0.8699
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.56959
4-1/M82	N/A	N/A
4-3-2/M82	1.10199
4-3/M82	0.94806	1
5-3/M82	1.27167	0.496
6-2/M82	0.99832	1
6-3/M82	1.04259
7-1/M82	N/A	N/A
7-2/M82	1.39165
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90694	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.81917
IL7-3/WTpooled	0.77101
IL12-4/WTpooled	0.99863	1
IL1-4/WTpooled	0.89803	0.699
WT/WTpooled	0.81738	0.764

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	1.26874	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82318	1
DC3000/delta hrp 6h	1.11747	1
DC3000/delta hrp 12h	1.13851	1
DC3000/delta hrp 24h	0.8605	0.126

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97634	1
DC3000 delta B/DC3000 delta AB	0.98936	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00654	1
Exp 36h	0.5341	0.406
Exp 60h	0.90982	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
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	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.97885	0.722
transgenic ySAMdc/azygous control (breaker)	0.8896	0.251
transgenic ySAMdc/azygous control (red)	1.07899	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.89276	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24165	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28366	0.14
Manapal/WT (break)	1.77014	0.123
Manapal/WT (red)	0.94629	0.728