Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02056	0.951
27DAP/17DAP	0.9926	1
39DAP/27DAP	0.99935	0.798
41DAP/39DAP	1.14291	0.202
42DAP/41DAP	0.81262	0.774
43DAP/42DAP	0.93202	0.867
47DAP/43DAP	1.20785	0.715
52DAP/47DAP	1.29609	0.588
57DAP/52DAP	0.95826	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81098	0.045
17DAP/reference	0.88919	0.129
27DAP/reference	0.85369	0.089
39DAP/reference	0.86118	0.2
41DAP/reference	0.7338	0.039
42DAP/reference	0.81995	0.017
43DAP/reference	0.88898	0.107
47DAP/reference	0.90265	0.05
52DAP/reference	1.00131	0.636
57DAP/reference	1.07058	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10186	0.841
27DAP/17DAP	1.1961	0.969
39DAP/27DAP	0.63166	0.215
41DAP/39DAP	1.08791	0.914
42DAP/41DAP	1.17317	1
43DAP/42DAP	1.28204	0.147
47DAP/43DAP	1.39523	0.293
52DAP/47DAP	1.00773	0.951
57DAP/52DAP	1.19806	0.654
57DAP/7DAP	0.8627

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1356	0.351
17DAP/reference	1.20508	0.162
27DAP/reference	1.31922	0.06
39DAP/reference	0.85718	0.146
41DAP/reference	0.92531	0.235
42DAP/reference	1.20648	0.059
43DAP/reference	1.23867	0.14
47DAP/reference	1.02622	0.98
52DAP/reference	1.07915	0.636
57DAP/reference	0.65097	0.028

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01774	0.979
17DAP/reference	0.87276	0.106
27DAP/reference	1.03366	0.765
39DAP/reference	1.07423	0.769
41DAP/reference	0.88576	0.115
42DAP/reference	0.84437	0.067
43DAP/reference	0.83811	0.032
47DAP/reference	1.03957	0.775
52DAP/reference	0.96388	0.469
57DAP/reference	1.00399	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34593	0.07
17DAP/reference	0.87885	0.308
27DAP/reference	0.96706	0.49
39DAP/reference	0.94927	0.328
41DAP/reference	0.97226	0.56
42DAP/reference	1.09403	0.333
43DAP/reference	1.13786	0.275
47DAP/reference	0.80037	0.06
52DAP/reference	1.54724	0.341
57DAP/reference	1.32069	0.056

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95917	1
26DAP/20DAP	1.02313	1
34DAP/26DAP	0.91127	0.861
51DAP/34DAP	1.43635	0.988
52DAP/51DAP	0.9287	1
53DAP/52DAP	0.9395	0.758
55DAP/53DAP	0.84241	0.577
57DAP/55DAP	0.94232	0.724
62DAP/57DAP	0.93225	0.871
68DAP/62DAP	2.08797	0.845
68DAP/14DAP	1.19301	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67268	0.047

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	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.75912
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.77449
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.97512
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12249	0.277
IL2-6/WTpooled	1.19079	0.659
IL7-5/WTpooled	1.48474	0.792
IL7-3/WTpooled	1.12861	1
IL12-4/WTpooled	1.19936	0.646
IL1-4/WTpooled	1.06512	1
WT/WTpooled	0.9623	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	0.95412	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05916	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18276	1
DC3000/delta hrp 24h	0.86692	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03543	1
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	6.37412	0.489
Exp 60h	1.59832	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06927	1
Var 0h	0.31457	1
Var 12h I row2-row1	1.16027	0.296
Var 12h NI row2-row1	1.8394	1
Var 36h I row2-row1	0.81365	1
Var 36h NI row2-row1	0.54393	0.743
Var 60h I row2-row1	0.92304	0.439
Var 60h NI row2-row1	0.72345	0.904
Time course 0hI-0hNI	0.98545	0.659
Time course 12hI-12hNI	1.19158	0.747
Time course 36hI-36hNI	1.67257	0.007
Time course 60hI-60hNI	2.3274	0.029

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)	1.17907	0.541
transgenic ySAMdc/azygous control (breaker)	1.21022	0.178
transgenic ySAMdc/azygous control (red)	1.00046	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96986	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22902	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99764	1
Manapal/WT (break)	0.52483	0.333
Manapal/WT (red)	0.84276	0.315