Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.18.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78311	0.195
27DAP/17DAP	1.31739	0.742
39DAP/27DAP	0.95497	0.663
41DAP/39DAP	1.60805	0.225
42DAP/41DAP	0.95892	1
43DAP/42DAP	0.96482	0.898
47DAP/43DAP	0.91398	0.699
52DAP/47DAP	1.46026	0.323
57DAP/52DAP	0.99043	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01717	1
17DAP/reference	0.97938	0.597
27DAP/reference	0.99924	0.904
39DAP/reference	1.03363	0.497
41DAP/reference	1.03353	0.714
42DAP/reference	1.06038	0.276
43DAP/reference	0.96563	0.41
47DAP/reference	0.97666	0.366
52DAP/reference	0.93376	0.189
57DAP/reference	0.88241	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91038	0.251
27DAP/17DAP	0.97482	0.854
39DAP/27DAP	1.06588	0.492
41DAP/39DAP	1.11272	0.674
42DAP/41DAP	0.96949	0.715
43DAP/42DAP	1.0288	0.585
47DAP/43DAP	1.0291	0.88
52DAP/47DAP	1.0227	0.927
57DAP/52DAP	0.98404	0.789
57DAP/7DAP	1.06993	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8364	0.115
17DAP/reference	0.76303	0.011
27DAP/reference	0.70145	0.01
39DAP/reference	0.8885	0.025
41DAP/reference	0.85033	0.06
42DAP/reference	0.84694	0.016
43DAP/reference	0.7087	0.011
47DAP/reference	0.81535	0.128
52DAP/reference	0.70016	0.012
57DAP/reference	0.81001	0.048

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05939	0.193
17DAP/reference	1.07121	0.191
27DAP/reference	1.02344	0.961
39DAP/reference	1.02527	0.912
41DAP/reference	0.97852	0.459
42DAP/reference	0.94057	0.067
43DAP/reference	1.00709	0.875
47DAP/reference	0.97537	0.5
52DAP/reference	1.07686	0.223
57DAP/reference	1.12174	0.296

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82474	0.049
17DAP/reference	0.91058	0.335
27DAP/reference	0.76966	0.033
39DAP/reference	0.71898	0.013
41DAP/reference	0.8999	0.025
42DAP/reference	0.79569	0.041
43DAP/reference	0.88723	0.033
47DAP/reference	0.96061	0.286
52DAP/reference	0.7568	0.155
57DAP/reference	0.85136	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94735	1
26DAP/20DAP	0.9529	0.512
34DAP/26DAP	1.04974	1
51DAP/34DAP	0.9732	0.791
52DAP/51DAP	0.97797	1
53DAP/52DAP	0.9601	0.811
55DAP/53DAP	1.05346	0.911
57DAP/55DAP	0.9529	0.78
62DAP/57DAP	0.96885	0.994
68DAP/62DAP	0.88898	0.464
68DAP/14DAP	1.09533	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92045	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.05084	0.058
Mature Green Tomato/Ripe Tomato	0.96375	0.66
Immature Eggplant/Mature Eggplant	2.77202	0.05
Ripe Pepper/Ripe Tomato	0.49927	0.224
Mature Eggplant/Ripe Tomato	2.18458	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01561	1
1-1-2/M82	0.99004	1
12-2/M82	1.00392	1
12-4/M82	0.99214
1-3/M82	0.87486	1
2-1-1/M82	1.25306
2-1/M82	N/A	N/A
2-6/M82	0.97761	1
3-2/M82	0.98895
4-1-1/M82	0.99015	1
4-1/M82	0.91759	1
4-3-2/M82	0.90777	0.698
4-3/M82	1.01905	1
5-3/M82	0.94039	1
6-2/M82	0.97991	1
6-3/M82	0.94078	0.916
7-1/M82	1.09386
7-2/M82	1.09637	1
9-3-2/M82	0.87561	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90632	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10102	1
IL12-4/WTpooled	1.16746	0.785
IL1-4/WTpooled	1.04015
WT/WTpooled	1.04877	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	2.17921	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07743	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.07677	1
DC3000/delta hrp 24h	1.11241	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97437	0.955
DC3000 delta B/DC3000 delta AB	1.05203	0.593

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.44139	0.254
Exp 36h	N/A	N/A
Exp 60h	1.30006	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01959	1
Var 0h	0.9161	1
Var 12h I row2-row1	1.6221	0.506
Var 12h NI row2-row1	1.03855	1
Var 36h I row2-row1	0.96362	1
Var 36h NI row2-row1	0.92336	0.706
Var 60h I row2-row1	1.15044	1
Var 60h NI row2-row1	1.22762	0.904
Time course 0hI-0hNI	1.0911	0.833
Time course 12hI-12hNI	1.06648	0.654
Time course 36hI-36hNI	1.17012	0.114
Time course 60hI-60hNI	1.33156	0.011

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)	1.66968	0.271
transgenic ySAMdc/azygous control (breaker)	0.81729	0.49
transgenic ySAMdc/azygous control (red)	1.18112	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99532	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80306	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.12063	0.105
Manapal/WT (break)	1.0824	1
Manapal/WT (red)	N/A	N/A