Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.3.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89543	0.568
27DAP/17DAP	1.25429	0.742
39DAP/27DAP	0.9175	0.631
41DAP/39DAP	1.13008	0.549
42DAP/41DAP	0.99253	1
43DAP/42DAP	1.05421	0.937
47DAP/43DAP	1.30691	0.474
52DAP/47DAP	0.94294	0.783
57DAP/52DAP	1.13139	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01934	0.994
17DAP/reference	1.38182	0.047
27DAP/reference	1.11638	0.285
39DAP/reference	1.06527	0.593
41DAP/reference	1.3603	0.067
42DAP/reference	1.12827	0.119
43DAP/reference	1.0608	1
47DAP/reference	1.08518	0.862
52DAP/reference	1.16459	0.149
57DAP/reference	0.86541	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02293	0.87
27DAP/17DAP	1.02103	0.951
39DAP/27DAP	0.95303	0.482
41DAP/39DAP	1.03054	0.774
42DAP/41DAP	1.05052	0.916
43DAP/42DAP	0.93384	0.206
47DAP/43DAP	0.98388	0.919
52DAP/47DAP	0.9527	0.694
57DAP/52DAP	0.88169	0.253
57DAP/7DAP	1.08914	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05282	1
17DAP/reference	0.9783	0.599
27DAP/reference	1.09237	0.371
39DAP/reference	0.97489	0.474
41DAP/reference	0.99186	0.512
42DAP/reference	0.8625	0.136
43DAP/reference	0.99173	0.637
47DAP/reference	1.02047	1
52DAP/reference	0.94931	0.363
57DAP/reference	0.91172	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51835	0.116
17DAP/reference	1.1157	0.723
27DAP/reference	1.19666	0.265
39DAP/reference	1.21056	0.207
41DAP/reference	1.13765	0.427
42DAP/reference	1.27764	0.053
43DAP/reference	1.1969	0.435
47DAP/reference	1.19977	0.016
52DAP/reference	1.36943	0.041
57DAP/reference	1.06659	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07652	0.32
17DAP/reference	1.13417	0.427
27DAP/reference	1.20775	0.357
39DAP/reference	1.01244	1
41DAP/reference	1.00028	0.826
42DAP/reference	1.30819	0.091
43DAP/reference	0.97901	0.59
47DAP/reference	0.91513	0.207
52DAP/reference	0.98212	0.732
57DAP/reference	0.90637	0.333

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08811	1
26DAP/20DAP	0.98365	1
34DAP/26DAP	0.87439	0.404
51DAP/34DAP	0.90927	0.513
52DAP/51DAP	1.08724	0.689
53DAP/52DAP	1.01215	1
55DAP/53DAP	0.98873	0.864
57DAP/55DAP	1.10534	0.915
62DAP/57DAP	1.30962	N/A
68DAP/62DAP	1.20568	N/A
68DAP/14DAP	0.76412	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01358	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.08455	N/A
Mature Green Tomato/Ripe Tomato	1.17163	0.185
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93742	N/A
12-2/M82	N/A	N/A
12-4/M82	0.72699	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.7824	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.04144	1
4-3-2/M82	0.82272	0.698
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.86561	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.47278	0.277
IL2-6/WTpooled	1.1862	0.584
IL7-5/WTpooled	1.59443	N/A
IL7-3/WTpooled	0.89478	1
IL12-4/WTpooled	1.19485	0.503
IL1-4/WTpooled	0.87448	0.699
WT/WTpooled	1.00439	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	1.17412	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85772	N/A
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.6554	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05169	0.648
DC3000 delta B/DC3000 delta AB	0.9292	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05261	1
Exp 36h	0.87759	0.879
Exp 60h	1.03807	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9938	1
Var 0h	0.90289	0.933
Var 12h I row2-row1	1.02852	0.58
Var 12h NI row2-row1	0.85239	0.546
Var 36h I row2-row1	1.04859	1
Var 36h NI row2-row1	1.06498	1
Var 60h I row2-row1	1.26494	1
Var 60h NI row2-row1	1.19096	0.904
Time course 0hI-0hNI	1.00228	1
Time course 12hI-12hNI	0.97676	0.698
Time course 36hI-36hNI	0.89486	0.097
Time course 60hI-60hNI	0.9232	0.319

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)	1.13965	0.431
transgenic ySAMdc/azygous control (breaker)	1.00657	1
transgenic ySAMdc/azygous control (red)	1.10418	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9066	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31956	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11414	1
Manapal/WT (break)	1.05265	1
Manapal/WT (red)	1.0947	1