Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33253	0.24
27DAP/17DAP	1.18259	0.799
39DAP/27DAP	1.17202	0.52
41DAP/39DAP	0.96828	0.825
42DAP/41DAP	1.17	0.894
43DAP/42DAP	0.99316	0.937
47DAP/43DAP	1.14658	0.497
52DAP/47DAP	0.96216	0.842
57DAP/52DAP	0.94393	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06556	0.611
17DAP/reference	0.97806	0.664
27DAP/reference	0.90247	0.137
39DAP/reference	1.04781	0.524
41DAP/reference	0.92741	0.341
42DAP/reference	0.90872	0.056
43DAP/reference	1.11137	0.142
47DAP/reference	1.0478	1
52DAP/reference	0.94362	0.341
57DAP/reference	1.0896	0.582

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06623	0.34
27DAP/17DAP	1.03248	0.885
39DAP/27DAP	1.04345	0.691
41DAP/39DAP	1.02661	0.827
42DAP/41DAP	1.03309	0.8
43DAP/42DAP	1.01939	0.664
47DAP/43DAP	0.98748	0.923
52DAP/47DAP	1.00713	0.986
57DAP/52DAP	0.97369	0.605
57DAP/7DAP	1.12371	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98904	0.682
17DAP/reference	0.96019	0.295
27DAP/reference	0.93456	0.058
39DAP/reference	0.99364	0.552
41DAP/reference	1.0969	0.042
42DAP/reference	1.03017	0.534
43DAP/reference	1.03487	0.408
47DAP/reference	1.02137	0.915
52DAP/reference	0.9418	0.137
57DAP/reference	1.07771	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11776	0.319
17DAP/reference	1.02337	0.739
27DAP/reference	1.25119	0.265
39DAP/reference	0.87161	0.156
41DAP/reference	0.92871	0.256
42DAP/reference	0.99518	0.655
43DAP/reference	1.4892	0.128
47DAP/reference	1.04105	0.73
52DAP/reference	0.96693	0.407
57DAP/reference	1.00541	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94414	0.054
17DAP/reference	1.04704	0.578
27DAP/reference	0.9786	0.319
39DAP/reference	1.00025	0.889
41DAP/reference	1.06513	0.357
42DAP/reference	0.95918	0.552
43DAP/reference	1.08612	0.25
47DAP/reference	1.03888	0.901
52DAP/reference	1.07634	0.575
57DAP/reference	0.84879	0.052

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88036	0.566
26DAP/20DAP	0.91505	0.317
34DAP/26DAP	0.95379	0.771
51DAP/34DAP	1.36748	0.047
52DAP/51DAP	0.91329	1
53DAP/52DAP	1.0723	0.806
55DAP/53DAP	0.85414	0.176
57DAP/55DAP	1.32477	0.51
62DAP/57DAP	1.21087	1
68DAP/62DAP	1.0044	0.939
68DAP/14DAP	1.07669	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20301	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.49199	0.103
Mature Green Tomato/Ripe Tomato	1.36552	0.016
Immature Eggplant/Mature Eggplant	1.09166	0.215
Ripe Pepper/Ripe Tomato	2.33562	0.258
Mature Eggplant/Ripe Tomato	1.08329	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26137	0.591
1-1-2/M82	1.12404	1
12-2/M82	0.88915
12-4/M82	1.06787	1
1-3/M82	1.31537	0.479
2-1-1/M82	0.84687	0.92
2-1/M82	N/A	N/A
2-6/M82	0.98004	1
3-2/M82	1.80762	0.717
4-1-1/M82	1.21734
4-1/M82	1.38705	0.853
4-3-2/M82	1.32956	0.508
4-3/M82	1.07807	1
5-3/M82	0.97755	1
6-2/M82	1.46256	1
6-3/M82	0.98991	1
7-1/M82	1.05013
7-2/M82	1.04909	1
9-3-2/M82	1.49626	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.78174	0.473
IL7-5/WTpooled	1.20058	1
IL7-3/WTpooled	0.88155	1
IL12-4/WTpooled	0.90305	1
IL1-4/WTpooled	0.95761	1
WT/WTpooled	1.0095	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	1.01551	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95693	1
DC3000/delta hrp 6h	0.88681	0.95
DC3000/delta hrp 12h	1.03263	1
DC3000/delta hrp 24h	1.12001	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17509	0.042
DC3000 delta B/DC3000 delta AB	1.15338	0.192

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.81926	0.699
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98976	1
Var 0h	1.13546	0.98
Var 12h I row2-row1	1.09833	0.254
Var 12h NI row2-row1	1.03641	1
Var 36h I row2-row1	1.1895	0.298
Var 36h NI row2-row1	0.92054	0.61
Var 60h I row2-row1	0.92186	0.374
Var 60h NI row2-row1	0.94323	0.572
Time course 0hI-0hNI	1.06553	0.764
Time course 12hI-12hNI	1.01995	0.786
Time course 36hI-36hNI	1.31297	0.007
Time course 60hI-60hNI	2.52315	0.01

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)	0.91571	0.428
transgenic ySAMdc/azygous control (breaker)	2.05219	0.161
transgenic ySAMdc/azygous control (red)	1.16051	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04976	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99883	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84645	1
Manapal/WT (break)	0.70397	0.333
Manapal/WT (red)	1.052	1