Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.1.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21115	0.477
27DAP/17DAP	2.28216	0.076
39DAP/27DAP	2.32536	0.03
41DAP/39DAP	0.80503	0.306
42DAP/41DAP	1.25512	0.871
43DAP/42DAP	1.10542	1
47DAP/43DAP	0.83448	0.496
52DAP/47DAP	0.79601	0.498
57DAP/52DAP	1.01933	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81668	0.125
17DAP/reference	0.76047	0.025
27DAP/reference	1.23164	0.051
39DAP/reference	1.08511	0.104
41DAP/reference	0.97287	0.667
42DAP/reference	2.02757	0.001
43DAP/reference	1.27532	0.287
47DAP/reference	1.56198	0.001
52DAP/reference	1.2832	0.016
57DAP/reference	1.12689	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22401	0.372
27DAP/17DAP	1.04709	0.938
39DAP/27DAP	1.44775	0.654
41DAP/39DAP	0.8813	0.793
42DAP/41DAP	1.28266	0.55
43DAP/42DAP	1.19962	0.212
47DAP/43DAP	1.547	0.331
52DAP/47DAP	1.05418	0.982
57DAP/52DAP	1.30176	0.315
57DAP/7DAP	1.46958	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72028	0.059
17DAP/reference	0.60722	0.011
27DAP/reference	1.12792	0.018
39DAP/reference	1.41979	0.009
41DAP/reference	1.38465	0.043
42DAP/reference	1.57937	0.03
43DAP/reference	2.01942	0.006
47DAP/reference	2.36957	0.014
52DAP/reference	1.72467	0.007
57DAP/reference	1.57962	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82074	0.028
17DAP/reference	0.7518	0.004
27DAP/reference	1.42311	0.051
39DAP/reference	1.30858	0.014
41DAP/reference	1.22368	0.038
42DAP/reference	1.34727	0.016
43DAP/reference	1.01232	0.774
47DAP/reference	1.09253	0.015
52DAP/reference	1.04206	0.528
57DAP/reference	1.02455	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67529	0.039
17DAP/reference	0.8548	0.452
27DAP/reference	0.80188	0.053
39DAP/reference	1.07891	0.733
41DAP/reference	0.89661	0.237
42DAP/reference	1.38094	0.02
43DAP/reference	1.61053	0.032
47DAP/reference	1.79505	0.006
52DAP/reference	1.98348	0.028
57DAP/reference	1.39418	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2125	0.966
26DAP/20DAP	1.01834	1
34DAP/26DAP	1.01128	1
51DAP/34DAP	0.97808	0.824
52DAP/51DAP	0.97935	1
53DAP/52DAP	0.88404	0.604
55DAP/53DAP	0.9191	0.675
57DAP/55DAP	1.12467	0.841
62DAP/57DAP	1.04015	0.935
68DAP/62DAP	1.00527	0.939
68DAP/14DAP	1.2749	0.161

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.79237	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.48778
Immature Eggplant/Mature Eggplant	4.5053	0.05
Ripe Pepper/Ripe Tomato	0.057	0.224
Mature Eggplant/Ripe Tomato	0.08125	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84173	0.69
1-1-2/M82	0.90412	1
12-2/M82	1.29138	0.61
12-4/M82	1.22201	1
1-3/M82	2.29352	0.248
2-1-1/M82	0.88901	0.465
2-1/M82	0.96184	1
2-6/M82	0.85951	1
3-2/M82	0.80242	0.455
4-1-1/M82	0.6094	1
4-1/M82	1.01572
4-3-2/M82	0.9536	1
4-3/M82	0.92128	1
5-3/M82	0.97526	1
6-2/M82	0.9067	0.481
6-3/M82	0.90621	1
7-1/M82	1.06489	1
7-2/M82	1.03372	1
9-3-2/M82	1.131	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07178	0.493
IL2-6/WTpooled	0.79833	0.473
IL7-5/WTpooled	0.751	1
IL7-3/WTpooled	1.16539	1
IL12-4/WTpooled	0.94293	1
IL1-4/WTpooled	1.05083	1
WT/WTpooled	1.05195	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	1.1786	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99013	1
DC3000/delta hrp 6h	1.70901	1
DC3000/delta hrp 12h	1.05512	1
DC3000/delta hrp 24h	0.95363	0.682

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9087	1
DC3000 delta B/DC3000 delta AB	0.53783	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93586	1
Exp 36h	2.86877	0.489
Exp 60h	1.3226	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.91925	1
Var 0h	0.68725	1
Var 12h I row2-row1	0.85798	0.627
Var 12h NI row2-row1	1.04655	1
Var 36h I row2-row1	1.11529	1
Var 36h NI row2-row1	1.59468	0.482
Var 60h I row2-row1	1.10904	1
Var 60h NI row2-row1	1.12259	0.904
Time course 0hI-0hNI	1.01839	0.852
Time course 12hI-12hNI	0.87714	0.106
Time course 36hI-36hNI	0.72546	0.023
Time course 60hI-60hNI	0.37659	0.006

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)	1.39674	0.326
transgenic ySAMdc/azygous control (breaker)	1.47701	1
transgenic ySAMdc/azygous control (red)	0.99467	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.69277	0.025

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.10602	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0158	1
Manapal/WT (break)	1.10035	1
Manapal/WT (red)	0.60104	0.181