Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.45128	0.014
27DAP/17DAP	1.03167	1
39DAP/27DAP	1.40777	0.191
41DAP/39DAP	1.05214	0.925
42DAP/41DAP	1.08071	0.999
43DAP/42DAP	1.15786	0.954
47DAP/43DAP	1.89386	0.228
52DAP/47DAP	1.83633	0.245
57DAP/52DAP	1.30391	0.787

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4128	0.031
17DAP/reference	0.6578	0.013
27DAP/reference	0.74043	0.052
39DAP/reference	0.85535	0.155
41DAP/reference	0.75761	0.039
42DAP/reference	1.2266	0.002
43DAP/reference	1.14578	0.163
47DAP/reference	2.4769	0.001
52DAP/reference	2.13709	0.007
57DAP/reference	1.91919	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72466	0.038
27DAP/17DAP	0.8871	0.58
39DAP/27DAP	0.94718	0.607
41DAP/39DAP	1.11364	0.753
42DAP/41DAP	0.98531	0.797
43DAP/42DAP	0.84883	0.026
47DAP/43DAP	1.27288	0.033
52DAP/47DAP	1.12929	0.57
57DAP/52DAP	1.23236	0.225
57DAP/7DAP	0.9751	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.61761	0.025
17DAP/reference	1.07693	0.477
27DAP/reference	1.02201	0.664
39DAP/reference	1.26466	0.038
41DAP/reference	1.31111	0.023
42DAP/reference	1.32724	0.014
43DAP/reference	1.55357	0.008
47DAP/reference	1.39762	0.026
52DAP/reference	1.33283	0.015
57DAP/reference	1.51722	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00959	0.884
17DAP/reference	0.74728	0.025
27DAP/reference	0.81127	0.123
39DAP/reference	0.94444	0.339
41DAP/reference	0.89684	0.098
42DAP/reference	0.9523	0.392
43DAP/reference	0.62419	0.032
47DAP/reference	1.06205	0.695
52DAP/reference	0.58537	0.005
57DAP/reference	0.80066	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58885	0.057
17DAP/reference	0.9569	0.56
27DAP/reference	0.78159	0.069
39DAP/reference	1.05568	0.792
41DAP/reference	1.06406	0.754
42DAP/reference	1.07215	0.671
43DAP/reference	1.1414	0.362
47DAP/reference	1.31559	0.055
52DAP/reference	1.76665	0.055
57DAP/reference	2.67667	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.78001	0.966
26DAP/20DAP	1.68633	0.118
34DAP/26DAP	0.54606	0.095
51DAP/34DAP	1.07398	0.637
52DAP/51DAP	0.78472	1
53DAP/52DAP	0.94972	0.79
55DAP/53DAP	0.88025	0.163
57DAP/55DAP	1.19295	0.826
62DAP/57DAP	0.60283
68DAP/62DAP	1.1365	0.646
68DAP/14DAP	0.65939	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42982	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.36918	0.068
Mature Green Tomato/Ripe Tomato	0.26236	0.017
Immature Eggplant/Mature Eggplant	1.52068	0.05
Ripe Pepper/Ripe Tomato	0.40892	0.224
Mature Eggplant/Ripe Tomato	0.40472	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11897	0.742
1-1-2/M82	1.35918	1
12-2/M82	0.98337	1
12-4/M82	1.02285	1
1-3/M82	2.19956	0.248
2-1-1/M82	0.86438	0.465
2-1/M82	0.60133
2-6/M82	0.98178	1
3-2/M82	0.98671
4-1-1/M82	1.33732	1
4-1/M82	0.642
4-3-2/M82	1.12922
4-3/M82	1.34101	0.268
5-3/M82	0.98344	1
6-2/M82	0.9012	0.481
6-3/M82	0.88549	0.916
7-1/M82	1.08809	1
7-2/M82	1.26228	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66899	0.321
IL2-6/WTpooled	1.04896	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95086	1
IL12-4/WTpooled	0.93561	1
IL1-4/WTpooled	0.93342	0.422
WT/WTpooled	0.92731	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	0.90602	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99273	1
DC3000/delta hrp 6h	1.13255	0.777
DC3000/delta hrp 12h	0.98091	1
DC3000/delta hrp 24h	0.87925	0.216

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16036	0.333
DC3000 delta B/DC3000 delta AB	0.88757	0.529

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2301	1
Exp 36h	1.05015	1
Exp 60h	0.94029	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95939	1
Var 0h	1.17748	1
Var 12h I row2-row1	0.85741	0.627
Var 12h NI row2-row1	1.37261	0.649
Var 36h I row2-row1	1.24437	0.283
Var 36h NI row2-row1	0.80994	0.645
Var 60h I row2-row1	0.72839	0.582
Var 60h NI row2-row1	0.93667	0.483
Time course 0hI-0hNI	0.81088	0.112
Time course 12hI-12hNI	1.04147	0.475
Time course 36hI-36hNI	1.0251	0.58
Time course 60hI-60hNI	1.36534	0.009

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)	0.74962	0.229
transgenic ySAMdc/azygous control (breaker)	0.87332	0.49
transgenic ySAMdc/azygous control (red)	1.01814	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.33785	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78198	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23392	0.105
Manapal/WT (break)	1.21085	1
Manapal/WT (red)	0.84956	0.181