Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82577	0.324
27DAP/17DAP	0.89475	0.758
39DAP/27DAP	1.13014	0.768
41DAP/39DAP	0.74798	0.258
42DAP/41DAP	1.4014	0.236
43DAP/42DAP	0.97161	0.909
47DAP/43DAP	0.91449	0.696
52DAP/47DAP	1.37036	0.828
57DAP/52DAP	1.09114	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17264	0.105
17DAP/reference	0.9354	0.419
27DAP/reference	0.96097	0.525
39DAP/reference	0.91649	0.298
41DAP/reference	0.72986	0.009
42DAP/reference	0.93237	0.145
43DAP/reference	0.91611	0.18
47DAP/reference	1.07259	0.167
52DAP/reference	0.96285	0.382
57DAP/reference	1.14565	0.159

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12423	0.365
27DAP/17DAP	0.8378	0.169
39DAP/27DAP	0.81068	0.103
41DAP/39DAP	1.54327	0.027
42DAP/41DAP	0.82833	0.145
43DAP/42DAP	0.78774	0.132
47DAP/43DAP	1.1111	0.618
52DAP/47DAP	1.01194	0.987
57DAP/52DAP	0.89472	0.322
57DAP/7DAP	0.56491	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36964	0.031
17DAP/reference	1.17677	0.221
27DAP/reference	1.07469	0.551
39DAP/reference	1.50103	0.023
41DAP/reference	1.10017	0.126
42DAP/reference	1.04368	0.889
43DAP/reference	1.10987	0.483
47DAP/reference	0.99559	1
52DAP/reference	0.98884	0.571
57DAP/reference	0.98023	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03263	0.687
17DAP/reference	0.89721	0.153
27DAP/reference	0.9814	0.554
39DAP/reference	1.08048	0.477
41DAP/reference	0.85581	0.124
42DAP/reference	0.91573	0.189
43DAP/reference	0.82058	0.039
47DAP/reference	0.86659	0.123
52DAP/reference	0.90453	0.093
57DAP/reference	0.791	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57913	0.027
17DAP/reference	1.11278	0.631
27DAP/reference	1.1467	0.447
39DAP/reference	1.09889	0.342
41DAP/reference	1.01017	0.826
42DAP/reference	1.18486	0.091
43DAP/reference	1.10268	0.465
47DAP/reference	1.05776	0.68
52DAP/reference	1.03648	0.862
57DAP/reference	0.98773	0.672

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.39609	0.966
26DAP/20DAP	0.81585	1
34DAP/26DAP	1.21662	1
51DAP/34DAP	0.88547	0.674
52DAP/51DAP	1.38704	0.197
53DAP/52DAP	1.29459	0.056
55DAP/53DAP	1.0083	0.917
57DAP/55DAP	1.13942	0.87
62DAP/57DAP	0.79615	0.088
68DAP/62DAP	1.67705	0.557
68DAP/14DAP	1.19872	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.54826	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45196	0.154
Mature Green Tomato/Ripe Tomato	1.63114	0.017
Immature Eggplant/Mature Eggplant	0.52199	0.062
Ripe Pepper/Ripe Tomato	0.57719	0.293
Mature Eggplant/Ripe Tomato	1.08865	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.33953
1-1-2/M82	1.38067	1
12-2/M82	0.86428	0.955
12-4/M82	1.02104	1
1-3/M82	N/A	N/A
2-1-1/M82	0.77687	0.465
2-1/M82	0.78646
2-6/M82	1.28391	0.385
3-2/M82	1.16991
4-1-1/M82	N/A	N/A
4-1/M82	3.60116
4-3-2/M82	N/A	N/A
4-3/M82	1.22526	0.268
5-3/M82	1.04979	1
6-2/M82	1.22254
6-3/M82	1.00178	1
7-1/M82	0.98968
7-2/M82	1.12471	0.318
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.51814
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98719	1
IL12-4/WTpooled	0.93301	1
IL1-4/WTpooled	1.14872	0.426
WT/WTpooled	1.03401	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	0.96555	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84503	0.941
DC3000/delta hrp 6h	1.02168	0.95
DC3000/delta hrp 12h	0.46386
DC3000/delta hrp 24h	0.71269	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24108	0.384
DC3000 delta B/DC3000 delta AB	2.12744	0.078

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85338	1
Exp 36h	0.69595	0.406
Exp 60h	0.64055	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00925	1
Var 0h	0.53556	0.936
Var 12h I row2-row1	0.85268	0.338
Var 12h NI row2-row1	1.06922	0.34
Var 36h I row2-row1	1.03131	1
Var 36h NI row2-row1	0.96769	0.706
Var 60h I row2-row1	0.85543	0.439
Var 60h NI row2-row1	1.04548	1
Time course 0hI-0hNI	0.9377	0.609
Time course 12hI-12hNI	1.06785	0.347
Time course 36hI-36hNI	1.09472	0.044
Time course 60hI-60hNI	7.43939	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)	1.32908	0.232
transgenic ySAMdc/azygous control (breaker)	0.97445	1
transgenic ySAMdc/azygous control (red)	1.20485	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95425	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95384	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.28918	0.084
Manapal/WT (break)	2.00437	0.14
Manapal/WT (red)	1.53691	0.222