Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.19.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11846	0.904
27DAP/17DAP	1.05877	0.92
39DAP/27DAP	0.86187	0.583
41DAP/39DAP	1.15878	0.597
42DAP/41DAP	1.21289	0.945
43DAP/42DAP	1.17441	0.772
47DAP/43DAP	1.39525	0.474
52DAP/47DAP	1.16063	1
57DAP/52DAP	1.32014	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20205	0.32
17DAP/reference	1.25248	0.172
27DAP/reference	1.42727	0.023
39DAP/reference	1.27298	0.046
41DAP/reference	1.52711	0.026
42DAP/reference	1.42466	0.001
43DAP/reference	1.32903	0.152
47DAP/reference	1.60025	0.001
52DAP/reference	1.47152	0.032
57DAP/reference	1.22177	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09748	0.525
27DAP/17DAP	1.10185	0.842
39DAP/27DAP	0.91617	0.371
41DAP/39DAP	1.278	0.417
42DAP/41DAP	0.7952	0.181
43DAP/42DAP	1.20748	0.192
47DAP/43DAP	1.12554	0.822
52DAP/47DAP	1.04072	0.883
57DAP/52DAP	0.9236	0.555
57DAP/7DAP	1.25754	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98279	0.613
17DAP/reference	0.78719	0.014
27DAP/reference	0.8033	0.018
39DAP/reference	1.11011	0.175
41DAP/reference	1.08602	0.325
42DAP/reference	1.10806	0.076
43DAP/reference	0.86326	0.061
47DAP/reference	1.45201	0.041
52DAP/reference	0.79517	0.021
57DAP/reference	0.76277	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10271	0.612
17DAP/reference	1.24367	0.658
27DAP/reference	1.05019	1
39DAP/reference	1.38013	0.05
41DAP/reference	1.39664	0.012
42DAP/reference	1.37849	0.076
43DAP/reference	1.18579	0.479
47DAP/reference	1.19076	0.042
52DAP/reference	1.34395	0.194
57DAP/reference	1.11539	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90023	0.268
17DAP/reference	0.88096	0.313
27DAP/reference	0.83136	0.052
39DAP/reference	1.05895	0.613
41DAP/reference	1.03331	0.618
42DAP/reference	1.24637	0.54
43DAP/reference	1.61862	0.05
47DAP/reference	2.31049	0.005
52DAP/reference	1.24589	0.205
57DAP/reference	1.53374	0.05

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.33008
26DAP/20DAP	1.0551	0.905
34DAP/26DAP	0.7497	0.272
51DAP/34DAP	1.1463	0.854
52DAP/51DAP	0.95279	1
53DAP/52DAP	1.2362	0.37
55DAP/53DAP	1.1208	0.368
57DAP/55DAP	1.11107	0.865
62DAP/57DAP	0.85032	0.681
68DAP/62DAP	0.61298	0.049
68DAP/14DAP	0.79043	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20821	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82013	0.274
Mature Green Tomato/Ripe Tomato	0.37226	0.026
Immature Eggplant/Mature Eggplant	0.54547	0.062
Ripe Pepper/Ripe Tomato	1.21822	1
Mature Eggplant/Ripe Tomato	0.83818	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.9474
12-2/M82	N/A	N/A
12-4/M82	1.06269	1
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.96337	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.93745
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.02805

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.59746
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	0.72018
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	0.94621	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.28287	1
DC3000/delta hrp 6h	1.05427	0.95
DC3000/delta hrp 12h	1.10145	1
DC3000/delta hrp 24h	0.97429	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41323
DC3000 delta B/DC3000 delta AB	1.46353	0.09

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.36631	1
Exp 36h	1.02146	0.943
Exp 60h	0.88581	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05092	1
Var 0h	1.31951	0.98
Var 12h I row2-row1	1.0246	0.795
Var 12h NI row2-row1	1.1927	0.34
Var 36h I row2-row1	0.98474	1
Var 36h NI row2-row1	0.78787	0.584
Var 60h I row2-row1	0.83816	0.374
Var 60h NI row2-row1	0.91019	0.483
Time course 0hI-0hNI	1.09079	0.764
Time course 12hI-12hNI	1.14118	0.085
Time course 36hI-36hNI	1.0934	0.114
Time course 60hI-60hNI	1.43112	0.008

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)	0.89899	0.3
transgenic ySAMdc/azygous control (breaker)	1.62645	0.172
transgenic ySAMdc/azygous control (red)	1.2368	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.912	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27021	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.72552	0.083
Manapal/WT (break)	2.39314	0.14
Manapal/WT (red)	0.9249	0.216