Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.8.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9072	0.568
27DAP/17DAP	1.29712	0.697
39DAP/27DAP	1.83907	0.054
41DAP/39DAP	0.9767	0.873
42DAP/41DAP	2.06993	0.126
43DAP/42DAP	1.56567	0.772
47DAP/43DAP	0.91112	0.687
52DAP/47DAP	0.87551	0.651
57DAP/52DAP	1.63658	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48684	0.025
17DAP/reference	0.55405	0.007
27DAP/reference	0.65111	0.012
39DAP/reference	1.09553	0.921
41DAP/reference	0.8337	0.085
42DAP/reference	2.04241	0.001
43DAP/reference	3.15617	0.006
47DAP/reference	3.94143	0.001
52DAP/reference	2.15953	0.011
57DAP/reference	2.00533	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07892	0.438
27DAP/17DAP	1.03492	0.957
39DAP/27DAP	0.98511	0.925
41DAP/39DAP	1.19548	0.79
42DAP/41DAP	1.11373	0.663
43DAP/42DAP	1.1058	0.094
47DAP/43DAP	0.9891	0.947
52DAP/47DAP	1.06182	0.819
57DAP/52DAP	1.27467	0.19
57DAP/7DAP	1.6294	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.99312	0.041
17DAP/reference	2.80713	0.006
27DAP/reference	3.14115	0.006
39DAP/reference	3.19196	0.005
41DAP/reference	3.09056	0.019
42DAP/reference	3.02134	0.006
43DAP/reference	3.7656	0.006
47DAP/reference	2.51888	0.2
52DAP/reference	3.61986	0.007
57DAP/reference	2.83658	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55842	0.009
17DAP/reference	0.42507	0.003
27DAP/reference	0.56162	0.007
39DAP/reference	0.5562	0.011
41DAP/reference	0.50488	0.007
42DAP/reference	0.58814	0.01
43DAP/reference	0.59246	0.017
47DAP/reference	1.20129	0.621
52DAP/reference	0.46186	0.003
57DAP/reference	0.74166	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0877	0.122
17DAP/reference	1.1604	0.763
27DAP/reference	2.1701	0.041
39DAP/reference	1.90303	0.104
41DAP/reference	1.97399	0.029
42DAP/reference	2.42405	0.006
43DAP/reference	3.37263	0.006
47DAP/reference	4.51861	0.005
52DAP/reference	4.04498	0.027
57DAP/reference	2.48586	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1542	0.966
26DAP/20DAP	1.37077	0.325
34DAP/26DAP	0.94433	0.936
51DAP/34DAP	1.07183	0.814
52DAP/51DAP	1.40689	0.304
53DAP/52DAP	0.89292	0.417
55DAP/53DAP	0.96324	0.746
57DAP/55DAP	0.86131	0.496
62DAP/57DAP	0.43713	0.028
68DAP/62DAP	0.97358	0.787
68DAP/14DAP	1.38844	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.19393	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.36364	0.078
Mature Green Tomato/Ripe Tomato	0.42074	0.019
Immature Eggplant/Mature Eggplant	2.43776	0.05
Ripe Pepper/Ripe Tomato	0.11342	0.224
Mature Eggplant/Ripe Tomato	0.03481	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3832	0.877
1-1-2/M82	1.42135	1
12-2/M82	1.14301	1
12-4/M82	2.11162	1
1-3/M82	2.52739	0.26
2-1-1/M82	0.87451	0.465
2-1/M82	0.95169	1
2-6/M82	0.95756	1
3-2/M82	0.20829	0.752
4-1-1/M82	1.13362	1
4-1/M82	0.43055
4-3-2/M82	1.33339	1
4-3/M82	0.96431	1
5-3/M82	0.95844	1
6-2/M82	1.25253	1
6-3/M82	0.92898	1
7-1/M82	1.03457	1
7-2/M82	1.30532	1
9-3-2/M82	1.37142	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93614	1
IL2-6/WTpooled	0.94742	1
IL7-5/WTpooled	2.04457	0.792
IL7-3/WTpooled	1.07069	1
IL12-4/WTpooled	0.8962	0.71
IL1-4/WTpooled	1.1266	0.426
WT/WTpooled	1.01625	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	1.00858	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94126	1
DC3000/delta hrp 6h	1.28845	1
DC3000/delta hrp 12h	1.10579	1
DC3000/delta hrp 24h	0.65876	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00049	1
DC3000 delta B/DC3000 delta AB	1.0627	0.593

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92739	1
Exp 36h	1.10912	1
Exp 60h	1.21906	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03272	1
Var 0h	1.01724	1
Var 12h I row2-row1	0.92797	0.514
Var 12h NI row2-row1	1.03866	1
Var 36h I row2-row1	1.01525	1
Var 36h NI row2-row1	1.44491	1
Var 60h I row2-row1	0.86428	0.287
Var 60h NI row2-row1	1.09186	0.904
Time course 0hI-0hNI	0.9966	1
Time course 12hI-12hNI	0.97812	0.858
Time course 36hI-36hNI	1.00072	0.826
Time course 60hI-60hNI	0.7866	0.047

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)	0.80651	0.428
transgenic ySAMdc/azygous control (breaker)	0.89852	1
transgenic ySAMdc/azygous control (red)	0.97808	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04833	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2985	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.98174	0.096
Manapal/WT (break)	1.01302	1
Manapal/WT (red)	1.52144	0.164