Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24908	0.443
27DAP/17DAP	1.69691	0.398
39DAP/27DAP	1.31095	0.927
41DAP/39DAP	1.2036	0.663
42DAP/41DAP	1.14747	0.898
43DAP/42DAP	1.40485	0.726
47DAP/43DAP	1.13019	1
52DAP/47DAP	1.25028	0.652
57DAP/52DAP	1.4667	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77237	0.07
17DAP/reference	0.91676	0.278
27DAP/reference	1.05971	0.934
39DAP/reference	1.11085	0.497
41DAP/reference	0.83594	0.026
42DAP/reference	0.9571	0.287
43DAP/reference	0.92586	0.346
47DAP/reference	1.03686	0.728
52DAP/reference	1.05348	0.951
57DAP/reference	1.18307	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25942	0.619
27DAP/17DAP	6.27072	0.339
39DAP/27DAP	1.05898	1
41DAP/39DAP	1.22092	0.887
42DAP/41DAP	0.84152	0.377
43DAP/42DAP	1.19664	1
47DAP/43DAP	1.14419	0.857
52DAP/47DAP	2.24523	0.293
57DAP/52DAP	1.24162	0.493
57DAP/7DAP	1.79207	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84688	0.146
17DAP/reference	0.8595	0.167
27DAP/reference	0.85239	0.042
39DAP/reference	0.82354	0.034
41DAP/reference	0.85108	0.166
42DAP/reference	0.92867	0.393
43DAP/reference	0.97096	0.48
47DAP/reference	0.99988	1
52DAP/reference	0.90859	0.15
57DAP/reference	0.88627	0.105

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97634	0.706
17DAP/reference	0.97862	0.548
27DAP/reference	0.8373	0.129
39DAP/reference	0.77974	0.117
41DAP/reference	0.99555	0.631
42DAP/reference	1.01914	1
43DAP/reference	1.06381	0.875
47DAP/reference	0.90944	0.227
52DAP/reference	1.01606	0.761
57DAP/reference	0.98478	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96249	0.455
17DAP/reference	0.99237	0.778
27DAP/reference	0.95924	0.49
39DAP/reference	0.97172	0.464
41DAP/reference	0.9055	0.209
42DAP/reference	0.97109	0.671
43DAP/reference	0.87188	0.143
47DAP/reference	0.98057	0.558
52DAP/reference	0.96519	0.611
57DAP/reference	0.87846	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11352	1
26DAP/20DAP	0.92587	1
34DAP/26DAP	1.43127	1
51DAP/34DAP	1.80839	0.149
52DAP/51DAP	1.08732	0.904
53DAP/52DAP	1.21792
55DAP/53DAP	1.13606	0.755
57DAP/55DAP	0.99496	0.953
62DAP/57DAP	0.99174	0.994
68DAP/62DAP	1.33909	0.507
68DAP/14DAP	1.11783	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.39542	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.42363	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96827
12-2/M82	N/A	N/A
12-4/M82	0.92673	0.358
1-3/M82	0.67913	0.441
2-1-1/M82	1.05644
2-1/M82	1.11258
2-6/M82	1.37639
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.85461
4-3/M82	1.70444	1
5-3/M82	0.72062	0.642
6-2/M82	1.31556	0.253
6-3/M82	0.9851	1
7-1/M82	N/A	N/A
7-2/M82	0.99812
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.75021	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9984	1
DC3000/delta hrp 6h	1.35046	1
DC3000/delta hrp 12h	1.08386	1
DC3000/delta hrp 24h	1.20358	0.123

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.4781	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0516	1
Exp 36h	1.28193	1
Exp 60h	0.98034	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.15932	1
Var 0h	1.27628	0.98
Var 12h I row2-row1	0.95045	0.856
Var 12h NI row2-row1	1.00538	1
Var 36h I row2-row1	0.64257	0.805
Var 36h NI row2-row1	1.15788	0.276
Var 60h I row2-row1	1.04689	1
Var 60h NI row2-row1	0.97377	1
Time course 0hI-0hNI	0.91003	0.867
Time course 12hI-12hNI	1.07165	0.803
Time course 36hI-36hNI	1.02428	0.316
Time course 60hI-60hNI	0.70917	0.006

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)	2.45502	0.292
transgenic ySAMdc/azygous control (breaker)	0.64275	0.139
transgenic ySAMdc/azygous control (red)	0.84589	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96134	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75378	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.51444	0.14
Manapal/WT (break)	1.04637	1
Manapal/WT (red)	1.18814	0.413