Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.1.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9886	0.83
27DAP/17DAP	2.03213	0.435
39DAP/27DAP	1.42723	0.699
41DAP/39DAP	1.69792	0.426
42DAP/41DAP	3.50992	0.016
43DAP/42DAP	2.77813	0.671
47DAP/43DAP	1.73262	0.215
52DAP/47DAP	0.41562	0.035
57DAP/52DAP	1.70629	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84713	0.025
17DAP/reference	0.79295	0.016
27DAP/reference	0.87068	0.032
39DAP/reference	0.91105	0.141
41DAP/reference	0.81389	0.01
42DAP/reference	1.33627	0.001
43DAP/reference	1.4671	0.022
47DAP/reference	1.36468	0.003
52DAP/reference	1.18844	0.108
57DAP/reference	1.14968	0.229

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10422	0.762
27DAP/17DAP	0.89459	0.537
39DAP/27DAP	1.05622	1
41DAP/39DAP	0.69428	0.072
42DAP/41DAP	1.47549	0.008
43DAP/42DAP	1.4736	0.014
47DAP/43DAP	1.449	0.017
52DAP/47DAP	1.5077	0.239
57DAP/52DAP	0.96277	0.697
57DAP/7DAP	2.04328	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64235	0.06
17DAP/reference	0.59491	0.011
27DAP/reference	0.73098	0.024
39DAP/reference	0.52414	0.011
41DAP/reference	0.57343	0.021
42DAP/reference	0.6917	0.05
43DAP/reference	1.40259	0.056
47DAP/reference	1.26322	0.182
52DAP/reference	0.81	0.072
57DAP/reference	0.49589	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92976	0.426
17DAP/reference	1.18069	0.338
27DAP/reference	1.12925	0.188
39DAP/reference	0.88666	0.243
41DAP/reference	0.97232	0.441
42DAP/reference	0.95892	0.433
43DAP/reference	0.81504	0.027
47DAP/reference	0.91079	0.05
52DAP/reference	0.88771	0.023
57DAP/reference	0.96652	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54407	0.044
17DAP/reference	0.82394	0.286
27DAP/reference	0.61376	0.032
39DAP/reference	0.70683	0.017
41DAP/reference	0.6506	0.07
42DAP/reference	1.92833	0.008
43DAP/reference	1.37206	0.015
47DAP/reference	1.58695	0.008
52DAP/reference	3.00449	0.028
57DAP/reference	1.09451	0.8

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10253	0.966
26DAP/20DAP	1.59308	0.39
34DAP/26DAP	1.45087	1
51DAP/34DAP	1.00317	0.835
52DAP/51DAP	2.82218	0.034
53DAP/52DAP	0.9134	0.677
55DAP/53DAP	1.49447	0.039
57DAP/55DAP	0.52431	0.031
62DAP/57DAP	1.09925	0.767
68DAP/62DAP	1.26662	0.737
68DAP/14DAP	1.34999	0.099

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65484	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	15.8439	0.058
Mature Green Tomato/Ripe Tomato	0.18536	0.017
Immature Eggplant/Mature Eggplant	0.84875	0.407
Ripe Pepper/Ripe Tomato	0.27169	0.293
Mature Eggplant/Ripe Tomato	0.32666	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99792	1
1-1-2/M82	1.80721	1
12-2/M82	0.90001	0.955
12-4/M82	1.6803	1
1-3/M82	2.90492	0.277
2-1-1/M82	0.97692	1
2-1/M82	0.91574	0.74
2-6/M82	1.1031	1
3-2/M82	1.53408	0.717
4-1-1/M82	0.61261
4-1/M82	0.83633
4-3-2/M82	N/A	N/A
4-3/M82	1.14887	1
5-3/M82	1.07659	1
6-2/M82	1.54538	1
6-3/M82	1.06341	1
7-1/M82	1.0266	1
7-2/M82	1.03317	1
9-3-2/M82	1.46426

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84175	0.243
IL2-6/WTpooled	0.97236	1
IL7-5/WTpooled	1.09962	1
IL7-3/WTpooled	0.71523	0.298
IL12-4/WTpooled	0.9884	1
IL1-4/WTpooled	1.03433	1
WT/WTpooled	1.05008	0.686

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	0.89944	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01582	0.921
DC3000/delta hrp 6h	1.08845	1
DC3000/delta hrp 12h	1.03876	1
DC3000/delta hrp 24h	0.78198	0.071

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04309
DC3000 delta B/DC3000 delta AB	1.22839	0.274

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83449	0.328
Exp 36h	0.91267	0.82
Exp 60h	0.77627	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.90217	1
Var 0h	0.9038	0.933
Var 12h I row2-row1	0.85874	0.363
Var 12h NI row2-row1	1.16194	1
Var 36h I row2-row1	0.97785	1
Var 36h NI row2-row1	1.6645	1
Var 60h I row2-row1	0.89836
Var 60h NI row2-row1	1.11732	0.701
Time course 0hI-0hNI	0.96056	0.738
Time course 12hI-12hNI	0.93016	0.39
Time course 36hI-36hNI	0.78256	0.026
Time course 60hI-60hNI	0.47634	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)	0.90813	0.529
transgenic ySAMdc/azygous control (breaker)	1.13718	0.248
transgenic ySAMdc/azygous control (red)	0.87699	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94558	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87152	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77562	1
Manapal/WT (break)	1.13295	0.381
Manapal/WT (red)	0.93386	0.503