Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.3.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03103	0.878
27DAP/17DAP	1.2046	0.833
39DAP/27DAP	0.94266	0.663
41DAP/39DAP	1.77792	0.243
42DAP/41DAP	0.92392	1
43DAP/42DAP	0.95172	0.863
47DAP/43DAP	1.13999	0.609
52DAP/47DAP	1.15744	0.902
57DAP/52DAP	1.00779	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8813	0.059
17DAP/reference	0.98303	0.701
27DAP/reference	0.98105	0.581
39DAP/reference	0.95208	0.381
41DAP/reference	1.06402	0.338
42DAP/reference	0.89603	0.013
43DAP/reference	0.89563	0.143
47DAP/reference	0.86598	0.005
52DAP/reference	0.88333	0.121
57DAP/reference	0.86518	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89152	0.376
27DAP/17DAP	1.10862	0.69
39DAP/27DAP	1.01411	0.854
41DAP/39DAP	1.01799	1
42DAP/41DAP	1.05282	0.861
43DAP/42DAP	1.07256	0.585
47DAP/43DAP	0.97562	0.861
52DAP/47DAP	1.02967	0.939
57DAP/52DAP	0.9544	0.637
57DAP/7DAP	1.06311	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89908	0.076
17DAP/reference	0.93758	0.021
27DAP/reference	0.9544	0.026
39DAP/reference	0.95929	0.064
41DAP/reference	0.89521	0.035
42DAP/reference	0.94073	0.106
43DAP/reference	0.94175	0.166
47DAP/reference	0.88017	0.128
52DAP/reference	0.89003	0.115
57DAP/reference	0.87729	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01257	0.952
17DAP/reference	0.94286	0.357
27DAP/reference	1.02366	0.619
39DAP/reference	0.86206	0.076
41DAP/reference	0.85035	0.071
42DAP/reference	0.83331	0.108
43DAP/reference	0.97579	0.592
47DAP/reference	0.9473	0.261
52DAP/reference	0.90872	0.101
57DAP/reference	1.03384	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9195	0.045
17DAP/reference	0.97714	0.647
27DAP/reference	0.94816	0.165
39DAP/reference	0.90595	0.037
41DAP/reference	0.90953	0.096
42DAP/reference	0.85708	0.172
43DAP/reference	0.9199	0.165
47DAP/reference	1.0219	0.994
52DAP/reference	0.92636	0.376
57DAP/reference	0.67767	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97337	1
26DAP/20DAP	0.95591	1
34DAP/26DAP	0.97212	0.94
51DAP/34DAP	1.065	0.654
52DAP/51DAP	1.00327	1
53DAP/52DAP	0.99674	0.998
55DAP/53DAP	1.03838	0.834
57DAP/55DAP	0.97957	0.867
62DAP/57DAP	1.02811	1
68DAP/62DAP	1.00692	0.834
68DAP/14DAP	1.1084	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93382	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.86826	0.377
Immature Eggplant/Mature Eggplant	1.09452	0.288
Ripe Pepper/Ripe Tomato	0.9515	N/A
Mature Eggplant/Ripe Tomato	1.5909	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01844	1
1-1-2/M82	0.96775	1
12-2/M82	1.12594	1
12-4/M82	1.02624	1
1-3/M82	0.98887	1
2-1-1/M82	1.36196	0.764
2-1/M82	N/A	N/A
2-6/M82	1.01315	1
3-2/M82	0.94947	0.752
4-1-1/M82	0.97832	1
4-1/M82	0.94127	1
4-3-2/M82	0.77171	0.487
4-3/M82	0.89505	1
5-3/M82	0.99046	1
6-2/M82	0.80169	N/A
6-3/M82	0.90447	0.982
7-1/M82	0.89261	N/A
7-2/M82	0.98456	1
9-3-2/M82	0.84794	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08251	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78779	0.294
IL12-4/WTpooled	1.21963	0.553
IL1-4/WTpooled	1.05994	0.426
WT/WTpooled	1.06161	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	0.95625	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03382	0.921
DC3000/delta hrp 6h	0.87343	0.95
DC3000/delta hrp 12h	1.29964	1
DC3000/delta hrp 24h	1.01485	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06325	0.25
DC3000 delta B/DC3000 delta AB	1.04473	0.544

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98669	1
Var 0h	0.43127	0.255
Var 12h I row2-row1	1.05653	0.544
Var 12h NI row2-row1	1.0335	1
Var 36h I row2-row1	0.88644	0.805
Var 36h NI row2-row1	1.02664	1
Var 60h I row2-row1	1.27655	1
Var 60h NI row2-row1	1.13524	0.904
Time course 0hI-0hNI	1.07202	0.662
Time course 12hI-12hNI	0.99579	1
Time course 36hI-36hNI	0.91361	0.25
Time course 60hI-60hNI	1.05936	0.495

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)	0.99053	0.862
transgenic ySAMdc/azygous control (breaker)	1.36594	0.178
transgenic ySAMdc/azygous control (red)	1.14443	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01917	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16236	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94905	0.172
Manapal/WT (break)	1.06674	1
Manapal/WT (red)	1.13666	0.413