Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79064	0.226
27DAP/17DAP	1.09551	0.872
39DAP/27DAP	1.41502	0.527
41DAP/39DAP	1.3675	0.535
42DAP/41DAP	1.34256	0.681
43DAP/42DAP	0.99201	0.931
47DAP/43DAP	1.49364	0.769
52DAP/47DAP	1.51459	0.298
57DAP/52DAP	1.36473	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05284	0.76
17DAP/reference	1.10204	0.161
27DAP/reference	1.02532	0.735
39DAP/reference	1.02499	0.691
41DAP/reference	1.01474	1
42DAP/reference	0.90421	0.02
43DAP/reference	0.91465	0.18
47DAP/reference	1.15477	0.114
52DAP/reference	1.08042	0.84
57DAP/reference	0.92417	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99579	0.763
27DAP/17DAP	0.99003	0.943
39DAP/27DAP	1.04234	1
41DAP/39DAP	1.20912	0.455
42DAP/41DAP	0.99873	0.819
43DAP/42DAP	0.77604	0.039
47DAP/43DAP	1.23228	0.094
52DAP/47DAP	0.95222	0.824
57DAP/52DAP	1.05496	0.891
57DAP/7DAP	0.86438	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.781	0.108
17DAP/reference	0.95473	0.338
27DAP/reference	0.98748	0.462
39DAP/reference	0.96287	0.411
41DAP/reference	0.96405	0.469
42DAP/reference	0.88111	0.117
43DAP/reference	0.97514	0.459
47DAP/reference	0.8816	0.168
52DAP/reference	0.81005	0.023
57DAP/reference	0.86269	0.128

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01104	0.97
17DAP/reference	1.01847	0.904
27DAP/reference	0.93277	0.34
39DAP/reference	0.88547	0.165
41DAP/reference	0.95022	0.299
42DAP/reference	0.89761	0.067
43DAP/reference	0.96278	0.486
47DAP/reference	0.99119	0.625
52DAP/reference	0.95028	0.302
57DAP/reference	0.88211	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08719	0.809
17DAP/reference	0.98238	0.681
27DAP/reference	1.01819	0.834
39DAP/reference	0.94794	0.393
41DAP/reference	1.08527	0.455
42DAP/reference	1.15634	0.408
43DAP/reference	0.87529	0.12
47DAP/reference	1.21552	0.085
52DAP/reference	1.07714	0.813
57DAP/reference	1.21894	0.428

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16109	0.966
26DAP/20DAP	1.61441	0.102
34DAP/26DAP	0.8724	0.771
51DAP/34DAP	0.84666	0.498
52DAP/51DAP	0.95793	1
53DAP/52DAP	1.0379	1
55DAP/53DAP	0.8727	0.243
57DAP/55DAP	1.00168	0.953
62DAP/57DAP	1.16501	0.8
68DAP/62DAP	0.79074	0.378
68DAP/14DAP	1.42085	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27664	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.17522	0.058
Mature Green Tomato/Ripe Tomato	1.00305	0.715
Immature Eggplant/Mature Eggplant	1.42971	0.05
Ripe Pepper/Ripe Tomato	1.0127	1
Mature Eggplant/Ripe Tomato	1.0377	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91739	0.651
1-1-2/M82	0.96744	1
12-2/M82	0.87553	0.862
12-4/M82	0.63177
1-3/M82	1.4185
2-1-1/M82	0.96421	0.565
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	1.05868	1
4-1/M82	N/A	N/A
4-3-2/M82	2.24054
4-3/M82	1.38217	1
5-3/M82	1.16432	0.572
6-2/M82	0.73609	0.481
6-3/M82	0.75072
7-1/M82	0.90934
7-2/M82	1.17871	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	0.88299	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.67409	0.427
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.06869	1
WT/WTpooled	N/A	N/A

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	0.92815	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15367	0.846
DC3000/delta hrp 6h	0.98113	0.95
DC3000/delta hrp 12h	0.83728	1
DC3000/delta hrp 24h	0.93397	0.523

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22668
DC3000 delta B/DC3000 delta AB	0.95262	0.71

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81555	1
Exp 36h	1.30595	0.693
Exp 60h	1.01952	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97242	1
Var 0h	0.91292	1
Var 12h I row2-row1	0.97646	0.948
Var 12h NI row2-row1	1.19412	0.649
Var 36h I row2-row1	1.18278	0.283
Var 36h NI row2-row1	0.86942	0.645
Var 60h I row2-row1	0.96271	0.439
Var 60h NI row2-row1	0.89371	0.408
Time course 0hI-0hNI	0.83035	0.074
Time course 12hI-12hNI	1.05812	0.743
Time course 36hI-36hNI	1.26287	0.218
Time course 60hI-60hNI	1.14866	0.16

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)	1.09428	0.325
transgenic ySAMdc/azygous control (breaker)	1.32375	0.178
transgenic ySAMdc/azygous control (red)	1.10255	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05286	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61252	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91768	1
Manapal/WT (break)	0.94848	1
Manapal/WT (red)	0.75007	0.242