Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98354	0.847
27DAP/17DAP	1.10283	0.92
39DAP/27DAP	0.77903	0.402
41DAP/39DAP	1.74476	0.28
42DAP/41DAP	1.01352	1
43DAP/42DAP	0.9804	0.93
47DAP/43DAP	1.11126	0.569
52DAP/47DAP	1.36411	0.436
57DAP/52DAP	0.9623	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90357	0.078
17DAP/reference	1.04192	0.33
27DAP/reference	1.01858	0.684
39DAP/reference	0.99161	0.874
41DAP/reference	0.99787	1
42DAP/reference	0.94149	0.111
43DAP/reference	1.03046	0.596
47DAP/reference	0.95764	0.098
52DAP/reference	0.72551	0.047
57DAP/reference	0.8677	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89928	0.47
27DAP/17DAP	1.03924	0.909
39DAP/27DAP	1.08612	0.483
41DAP/39DAP	0.98189	0.997
42DAP/41DAP	1.05445	0.727
43DAP/42DAP	1.01263	0.83
47DAP/43DAP	1.03138	0.837
52DAP/47DAP	1.0523	0.856
57DAP/52DAP	0.98122	0.756
57DAP/7DAP	1.09596	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93494	0.138
17DAP/reference	0.95383	0.072
27DAP/reference	0.91538	0.082
39DAP/reference	0.96059	0.307
41DAP/reference	0.9176	0.056
42DAP/reference	0.81878	0.014
43DAP/reference	0.94419	0.11
47DAP/reference	0.89602	0.293
52DAP/reference	0.79479	0.023
57DAP/reference	1.08122	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01297	0.943
17DAP/reference	0.97143	0.461
27DAP/reference	0.8699	0.139
39DAP/reference	0.85038	0.105
41DAP/reference	0.88117	0.137
42DAP/reference	0.93304	0.261
43DAP/reference	0.96224	0.423
47DAP/reference	0.96352	0.284
52DAP/reference	0.93935	0.171
57DAP/reference	0.98239	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89271	0.119
17DAP/reference	0.92142	0.186
27DAP/reference	1.02908	0.531
39DAP/reference	0.97623	0.504
41DAP/reference	0.99274	0.754
42DAP/reference	0.92886	0.361
43DAP/reference	0.91046	0.206
47DAP/reference	0.89391	0.153
52DAP/reference	0.90132	0.31
57DAP/reference	0.65375	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00282	1
26DAP/20DAP	0.93303	1
34DAP/26DAP	0.97344	0.92
51DAP/34DAP	1.03957	0.73
52DAP/51DAP	1.01031	0.888
53DAP/52DAP	1.02967	0.882
55DAP/53DAP	1.04373	0.948
57DAP/55DAP	1.03916	0.986
62DAP/57DAP	1.0796	0.678
68DAP/62DAP	1.20082	0.657
68DAP/14DAP	1.21136	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04016	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.88309	0.226
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95024	0.944
1-1-2/M82	0.95459	1
12-2/M82	0.9371	0.74
12-4/M82	1.00096	1
1-3/M82	0.96097	0.501
2-1-1/M82	1.18545	1
2-1/M82	N/A	N/A
2-6/M82	0.9574	1
3-2/M82	0.86628	0.752
4-1-1/M82	0.96334	1
4-1/M82	1.02004	1
4-3-2/M82	0.98822	1
4-3/M82	1.16136	1
5-3/M82	1.08585	1
6-2/M82	1.03768	0.195
6-3/M82	0.97348	1
7-1/M82	0.97112
7-2/M82	1.1168	1
9-3-2/M82	0.83025	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95649	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9866	1
IL12-4/WTpooled	0.90396	0.71
IL1-4/WTpooled	1.10543
WT/WTpooled	1.00262	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	1.35956	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95077	0.941
DC3000/delta hrp 6h	0.96586
DC3000/delta hrp 12h	1.1378	1
DC3000/delta hrp 24h	1.09209	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08373	0.134
DC3000 delta B/DC3000 delta AB	1.09057	0.372

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.52159	0.227
Exp 36h	1.71418	0.489
Exp 60h	2.04663	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00702	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.06411	0.473
Var 12h NI row2-row1	0.99441	1
Var 36h I row2-row1	0.92279	1
Var 36h NI row2-row1	0.87186	0.549
Var 60h I row2-row1	1.07913	1
Var 60h NI row2-row1	1.05278	1
Time course 0hI-0hNI	1.12479	0.662
Time course 12hI-12hNI	1.07807	0.593
Time course 36hI-36hNI	1.2126	0.007
Time course 60hI-60hNI	2.1853	0.008

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	2.1651	1
transgenic ySAMdc/azygous control (red)	1.9406	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97545	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.46708	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.98349	1
Manapal/WT (red)	0.96591	0.728