Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74028	0.056
27DAP/17DAP	0.79931	0.452
39DAP/27DAP	1.00151	0.782
41DAP/39DAP	0.93426	0.724
42DAP/41DAP	1.03173	1
43DAP/42DAP	0.958	0.906
47DAP/43DAP	1.02846	1
52DAP/47DAP	0.99754	0.72
57DAP/52DAP	1.00841	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9527	0.455
17DAP/reference	0.99809	0.904
27DAP/reference	1.12853	0.156
39DAP/reference	0.95075	0.437
41DAP/reference	0.91069	0.201
42DAP/reference	0.88552	0.014
43DAP/reference	1.00279	1
47DAP/reference	1.08904	0.524
52DAP/reference	0.86917	0.131
57DAP/reference	1.01424	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16818	0.252
27DAP/17DAP	0.96639	0.878
39DAP/27DAP	1.01552	0.862
41DAP/39DAP	1.15002	0.579
42DAP/41DAP	0.88877	0.267
43DAP/42DAP	0.91626	0.256
47DAP/43DAP	0.97143	0.857
52DAP/47DAP	0.96707	0.899
57DAP/52DAP	1.10689	0.518
57DAP/7DAP	1.38917	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85869	0.115
17DAP/reference	0.87155	0.044
27DAP/reference	0.9468	0.159
39DAP/reference	1.00573	0.745
41DAP/reference	1.01148	0.848
42DAP/reference	1.01124	0.751
43DAP/reference	0.93021	0.23
47DAP/reference	0.91901	0.383
52DAP/reference	1.08496	0.599
57DAP/reference	1.13995	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29422	0.193
17DAP/reference	1.07678	0.518
27DAP/reference	1.04013	1
39DAP/reference	1.00719	0.682
41DAP/reference	1.08641	0.344
42DAP/reference	0.98426	0.594
43DAP/reference	1.24902	0.276
47DAP/reference	1.0514	0.751
52DAP/reference	0.85976	0.018
57DAP/reference	1.15888	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92167	0.249
17DAP/reference	0.99088	0.763
27DAP/reference	1.0269	0.903
39DAP/reference	1.16914	0.009
41DAP/reference	0.97969	0.682
42DAP/reference	0.97917	0.552
43DAP/reference	0.87178	0.171
47DAP/reference	1.04498	0.792
52DAP/reference	0.90351	0.36
57DAP/reference	1.0714	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01593	1
26DAP/20DAP	1.09325	0.865
34DAP/26DAP	0.98522	1
51DAP/34DAP	1.00625	0.927
52DAP/51DAP	1.13305	0.078
53DAP/52DAP	1.10275	0.783
55DAP/53DAP	1.15848	0.589
57DAP/55DAP	1.12487	0.898
62DAP/57DAP	1.19694	0.8
68DAP/62DAP	1.32553	0.077
68DAP/14DAP	0.92574	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07578	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.19904	0.075
Mature Green Tomato/Ripe Tomato	0.72204	0.086
Immature Eggplant/Mature Eggplant	0.72571	0.092
Ripe Pepper/Ripe Tomato	1.00612	1
Mature Eggplant/Ripe Tomato	1.34275	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00261	1
1-1-2/M82	0.98971
12-2/M82	0.83134	0.955
12-4/M82	0.79438	0.33
1-3/M82	1.32151
2-1-1/M82	0.66805	0.465
2-1/M82	0.93857
2-6/M82	0.83409	0.501
3-2/M82	N/A	N/A
4-1-1/M82	1.06913
4-1/M82	N/A	N/A
4-3-2/M82	0.64582
4-3/M82	0.72908	0.578
5-3/M82	1.16244	1
6-2/M82	0.45567
6-3/M82	0.92785	1
7-1/M82	N/A	N/A
7-2/M82	1.02206
9-3-2/M82	0.78027

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89768
IL2-6/WTpooled	1.11959	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88269	0.294
IL12-4/WTpooled	1.11736	0.595
IL1-4/WTpooled	1.0543
WT/WTpooled	0.99477	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	1.0267	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.35928	0.921
DC3000/delta hrp 6h	0.99012	0.95
DC3000/delta hrp 12h	1.05637	1
DC3000/delta hrp 24h	0.97288	0.897

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	1.14105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80953	1
Exp 36h	1.68324	0.409
Exp 60h	1.30565	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04844	1
Var 0h	0.81252	0.332
Var 12h I row2-row1	1.13172	0.736
Var 12h NI row2-row1	1.68961	0.281
Var 36h I row2-row1	0.92167	1
Var 36h NI row2-row1	0.3568	0.421
Var 60h I row2-row1	1.05308	0.562
Var 60h NI row2-row1	1.03773	1
Time course 0hI-0hNI	0.75742	0.095
Time course 12hI-12hNI	1.02233	0.818
Time course 36hI-36hNI	1.73124	0.028
Time course 60hI-60hNI	1.30463	0.426

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)	1.13051	0.287
transgenic ySAMdc/azygous control (breaker)	1.67247	0.248
transgenic ySAMdc/azygous control (red)	1.21576	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01084	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90078	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98653	1
Manapal/WT (break)	1.04189	1
Manapal/WT (red)	0.90768	0.274