Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86886	0.445
27DAP/17DAP	0.98332	0.994
39DAP/27DAP	1.29069	0.4
41DAP/39DAP	1.07295	0.78
42DAP/41DAP	1.66821	0.587
43DAP/42DAP	1.23042	0.607
47DAP/43DAP	1.26381	0.689
52DAP/47DAP	1.16638	0.948
57DAP/52DAP	0.92233	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8996	0.041
17DAP/reference	0.94933	0.342
27DAP/reference	0.95829	0.249
39DAP/reference	0.91175	0.093
41DAP/reference	0.91332	0.201
42DAP/reference	0.79445	0.001
43DAP/reference	0.92773	0.113
47DAP/reference	0.85923	0.011
52DAP/reference	1.26591	0.134
57DAP/reference	1.03597	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14708	0.298
27DAP/17DAP	1.08819	0.915
39DAP/27DAP	1.10936	0.603
41DAP/39DAP	0.83351	0.361
42DAP/41DAP	1.03282	1
43DAP/42DAP	1.16416	0.25
47DAP/43DAP	0.95339	0.796
52DAP/47DAP	1.15123	0.568
57DAP/52DAP	1.04118	0.776
57DAP/7DAP	1.11994	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14768	0.351
17DAP/reference	0.88604	0.094
27DAP/reference	1.05252	0.974
39DAP/reference	1.19049	0.066
41DAP/reference	0.74975	0.023
42DAP/reference	0.8788	0.178
43DAP/reference	0.95288	0.252
47DAP/reference	0.98263	0.671
52DAP/reference	0.75019	0.04
57DAP/reference	0.98357	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00415	0.993
17DAP/reference	0.81496	0.02
27DAP/reference	0.91128	0.15
39DAP/reference	0.89465	0.129
41DAP/reference	0.95967	0.315
42DAP/reference	0.83864	0.023
43DAP/reference	0.8863	0.111
47DAP/reference	0.82865	0.015
52DAP/reference	0.90674	0.06
57DAP/reference	0.79397	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77543	0.057
17DAP/reference	0.94211	0.407
27DAP/reference	0.96042	0.357
39DAP/reference	0.94715	0.328
41DAP/reference	0.82987	0.148
42DAP/reference	1.09068	0.635
43DAP/reference	0.88982	0.064
47DAP/reference	0.92905	0.161
52DAP/reference	1.21439	0.448
57DAP/reference	1.121	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9523	0.997
26DAP/20DAP	0.76865	0.228
34DAP/26DAP	0.84281	0.419
51DAP/34DAP	1.13824	0.445
52DAP/51DAP	0.87408	1
53DAP/52DAP	1.02161	0.921
55DAP/53DAP	0.85295	0.303
57DAP/55DAP	1.06398	0.947
62DAP/57DAP	0.90927	0.681
68DAP/62DAP	1.34191	0.345
68DAP/14DAP	1.2003	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79391	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1222	0.287
Mature Green Tomato/Ripe Tomato	0.47561	0.023
Immature Eggplant/Mature Eggplant	0.80549	0.223
Ripe Pepper/Ripe Tomato	0.95982	1
Mature Eggplant/Ripe Tomato	0.54095	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.34765	0.591
1-1-2/M82	1.20946	1
12-2/M82	0.90059	0.955
12-4/M82	0.72658	0.33
1-3/M82	N/A	N/A
2-1-1/M82	1.10641	0.422
2-1/M82	1.21569	0.345
2-6/M82	1.06051
3-2/M82	0.96979	1
4-1-1/M82	0.90661	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.31107	1
5-3/M82	1.16046	0.378
6-2/M82	0.86644
6-3/M82	0.56033	1
7-1/M82	1.06224	0.598
7-2/M82	0.90866	0.881
9-3-2/M82	0.93305

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.2554	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8839	1
IL12-4/WTpooled	1.02094	0.891
IL1-4/WTpooled	0.92887
WT/WTpooled	0.98244	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	1.05016	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87676	1
DC3000/delta hrp 6h	0.91303	0.95
DC3000/delta hrp 12h	0.8892	1
DC3000/delta hrp 24h	0.81367	0.087

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51865
DC3000 delta B/DC3000 delta AB	3.74153	0.13

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02347	1
Exp 36h	0.90585	0.749
Exp 60h	0.95195	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00346	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.97736	0.948
Var 12h NI row2-row1	1.1176	1
Var 36h I row2-row1	1.23302	0.489
Var 36h NI row2-row1	0.96494	0.791
Var 60h I row2-row1	0.85342	0.439
Var 60h NI row2-row1	1.07386	0.904
Time course 0hI-0hNI	1.13881	0.574
Time course 12hI-12hNI	0.90131	0.144
Time course 36hI-36hNI	0.87853	0.112
Time course 60hI-60hNI	0.64182	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)	1.03501	0.384
transgenic ySAMdc/azygous control (breaker)	1.52421	0.162
transgenic ySAMdc/azygous control (red)	1.04004	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14911	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88483	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.4569	0.093
Manapal/WT (break)	0.79315	1
Manapal/WT (red)	0.7723	0.184