Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.1.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69468	0.042
27DAP/17DAP	1.14629	0.859
39DAP/27DAP	1.08044	0.841
41DAP/39DAP	1.17493	0.549
42DAP/41DAP	1.26444	0.712
43DAP/42DAP	1.06014	1
47DAP/43DAP	1.08602	0.555
52DAP/47DAP	0.93951	0.799
57DAP/52DAP	0.91264	0.899

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1403	0.021
17DAP/reference	1.06517	0.412
27DAP/reference	0.91474	0.106
39DAP/reference	0.98334	0.762
41DAP/reference	1.06462	0.365
42DAP/reference	1.07216	0.045
43DAP/reference	1.05158	0.646
47DAP/reference	1.10912	0.13
52DAP/reference	0.91048	0.091
57DAP/reference	0.92134	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0795	0.547
27DAP/17DAP	1.06936	0.859
39DAP/27DAP	0.84971	0.239
41DAP/39DAP	1.09778	0.484
42DAP/41DAP	1.24814	0.036
43DAP/42DAP	1.06523	0.83
47DAP/43DAP	0.94296	0.764
52DAP/47DAP	0.98643	0.907
57DAP/52DAP	1.35374	0.165
57DAP/7DAP	0.65564	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16227	0.351
17DAP/reference	0.99924	0.518
27DAP/reference	1.28516	0.246
39DAP/reference	0.969	0.474
41DAP/reference	0.85657	0.058
42DAP/reference	0.95119	0.415
43DAP/reference	0.77572	0.025
47DAP/reference	1.06883	0.915
52DAP/reference	0.83548	0.057
57DAP/reference	0.84704	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27393	0.038
17DAP/reference	1.27181	0.271
27DAP/reference	1.11506	0.67
39DAP/reference	0.95518	0.339
41DAP/reference	1.06407	0.846
42DAP/reference	1.0415	0.826
43DAP/reference	1.03396	1
47DAP/reference	0.98908	0.59
52DAP/reference	0.90296	0.111
57DAP/reference	0.76405	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96955	0.422
17DAP/reference	1.17686	0.105
27DAP/reference	1.10217	0.834
39DAP/reference	1.02043	1
41DAP/reference	1.12027	0.471
42DAP/reference	1.09686	0.54
43DAP/reference	0.85819	0.137
47DAP/reference	0.96721	0.465
52DAP/reference	0.9917	0.8
57DAP/reference	1.18247	0.623

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.36671	0.966
26DAP/20DAP	1.27896	0.39
34DAP/26DAP	1.01655	1
51DAP/34DAP	1.38436	0.1
52DAP/51DAP	1.16893	0.213
53DAP/52DAP	1.10616	0.882
55DAP/53DAP	0.79419	0.077
57DAP/55DAP	0.90293	0.724
62DAP/57DAP	1.14865	N/A
68DAP/62DAP	1.12918	0.95
68DAP/14DAP	1.09105	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10644	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.59749	0.06
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.06714	0.224
Mature Eggplant/Ripe Tomato	0.06461	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.09889	N/A
12-2/M82	N/A	N/A
12-4/M82	0.92118	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
4-1/M82	1.93968	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.15395	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.62881	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83301	0.247
IL2-6/WTpooled	1.71941	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.53425	1
IL12-4/WTpooled	0.97614	1
IL1-4/WTpooled	1.22625	1
WT/WTpooled	1.16155	0.855

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	1.18615	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03059	0.921
DC3000/delta hrp 6h	0.99164	0.95
DC3000/delta hrp 12h	1.0091	1
DC3000/delta hrp 24h	1.09433	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.28224	0.515
DC3000 delta B/DC3000 delta AB	0.97726	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86491	1
Exp 36h	0.93879	0.879
Exp 60h	0.86912	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.90338	1
Var 0h	0.65475	1
Var 12h I row2-row1	1.02693	0.795
Var 12h NI row2-row1	0.88617	0.488
Var 36h I row2-row1	1.03885	0.908
Var 36h NI row2-row1	1.06447	1
Var 60h I row2-row1	1.56729	1
Var 60h NI row2-row1	1.21309	0.631
Time course 0hI-0hNI	1.04503	0.852
Time course 12hI-12hNI	0.93142	0.53
Time course 36hI-36hNI	0.83005	0.19
Time course 60hI-60hNI	1.08224	0.426

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)	1.05742	0.511
transgenic ySAMdc/azygous control (breaker)	1.03009	1
transgenic ySAMdc/azygous control (red)	0.98064	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03148	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12693	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47471	0.14
Manapal/WT (break)	1.04053	1
Manapal/WT (red)	0.652	0.181