Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.4.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05689	0.977
27DAP/17DAP	1.00651	1
39DAP/27DAP	1.45976	0.165
41DAP/39DAP	1.49145	0.225
42DAP/41DAP	2.30691	0.016
43DAP/42DAP	1.34561	0.321
47DAP/43DAP	1.56557	0.4
52DAP/47DAP	0.66886	0.185
57DAP/52DAP	1.11679	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.49842	0.027
17DAP/reference	0.62088	0.017
27DAP/reference	0.67589	0.017
39DAP/reference	0.99052	0.734
41DAP/reference	0.8803	0.267
42DAP/reference	1.57606	0.001
43DAP/reference	1.72408	0.007
47DAP/reference	2.45098	0.001
52DAP/reference	1.56443	0.036
57DAP/reference	1.28587	0.088

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1727	0.298
27DAP/17DAP	1.18622	0.505
39DAP/27DAP	1.10663	0.677
41DAP/39DAP	1.07246	1
42DAP/41DAP	1.08557	0.81
43DAP/42DAP	1.07007	0.627
47DAP/43DAP	1.02903	0.95
52DAP/47DAP	1.0829	0.856
57DAP/52DAP	1.31948	0.219
57DAP/7DAP	1.20466	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83084	0.27
17DAP/reference	1.39281	0.574
27DAP/reference	0.76959	0.264
39DAP/reference	1.27268	0.411
41DAP/reference	1.29056	0.389
42DAP/reference	0.90603	0.235
43DAP/reference	0.85716	0.11
47DAP/reference	1.33015	0.304
52DAP/reference	1.19563	0.183
57DAP/reference	0.91407	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47059	0.006
17DAP/reference	0.46579	0.004
27DAP/reference	0.79291	0.173
39DAP/reference	0.55584	0.009
41DAP/reference	0.59229	0.018
42DAP/reference	0.60214	0.013
43DAP/reference	0.63004	0.003
47DAP/reference	0.79748	0.019
52DAP/reference	0.49385	0.003
57DAP/reference	0.57942	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89585	0.335
17DAP/reference	0.55736	0.172
27DAP/reference	0.57683	N/A
39DAP/reference	1.84737	0.987
41DAP/reference	1.03666	1
42DAP/reference	1.36227	0.175
43DAP/reference	1.62997	0.039
47DAP/reference	3.13313	0.005
52DAP/reference	2.26078	0.082
57DAP/reference	2.06016	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11659	0.966
26DAP/20DAP	2.47842	0.099
34DAP/26DAP	0.73917	0.119
51DAP/34DAP	1.2382	0.066
52DAP/51DAP	0.91859	1
53DAP/52DAP	1.06079	0.783
55DAP/53DAP	0.67609	0.037
57DAP/55DAP	1.3907	0.231
62DAP/57DAP	0.93733	0.871
68DAP/62DAP	1.05771	0.956
68DAP/14DAP	1.32802	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78103	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.2078	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.4961	0.293
Mature Eggplant/Ripe Tomato	0.92214	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15419	0.526
1-1-2/M82	1.36361	1
12-2/M82	0.85296	0.955
12-4/M82	1.62139	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	1.20941	0.967
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.86057	1
4-3/M82	1.40084	1
5-3/M82	0.98912	1
6-2/M82	1.66579	N/A
6-3/M82	1.27146	1
7-1/M82	1.00955	1
7-2/M82	1.03555	N/A
9-3-2/M82	1.15294	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8245	0.243
IL2-6/WTpooled	1.09111	0.788
IL7-5/WTpooled	1.08047	1
IL7-3/WTpooled	1.01541	1
IL12-4/WTpooled	1.49237	0.673
IL1-4/WTpooled	1.12099	1
WT/WTpooled	0.98453	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	1.18085	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87923	0.734
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.02403	1
DC3000/delta hrp 24h	1.35328	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29345	0.076
DC3000 delta B/DC3000 delta AB	1.11264	0.363

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.70906	1
Exp 36h	1.33384	1
Exp 60h	0.97191	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02718	1
Var 0h	0.87895	1
Var 12h I row2-row1	1.02024	1
Var 12h NI row2-row1	1.2279	0.266
Var 36h I row2-row1	1.19651	0.41
Var 36h NI row2-row1	0.82827	0.478
Var 60h I row2-row1	0.71281	0.292
Var 60h NI row2-row1	0.93007	0.977
Time course 0hI-0hNI	0.96969	0.849
Time course 12hI-12hNI	1.09029	0.503
Time course 36hI-36hNI	1.48258	0.005
Time course 60hI-60hNI	1.81756	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)	0.45032	0.227
transgenic ySAMdc/azygous control (breaker)	0.8365	0.49
transgenic ySAMdc/azygous control (red)	1.05096	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99907	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96547	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.48999	0.172
Manapal/WT (break)	1.22584	0.381
Manapal/WT (red)	1.12365	1