Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06801	0.997
27DAP/17DAP	1.12508	0.872
39DAP/27DAP	1.02182	1
41DAP/39DAP	1.08767	0.535
42DAP/41DAP	3.22983	0.031
43DAP/42DAP	1.107	1
47DAP/43DAP	1.12315	0.793
52DAP/47DAP	0.67136	0.213
57DAP/52DAP	1.29544	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7056	0.041
17DAP/reference	1.00485	0.907
27DAP/reference	0.85733	0.022
39DAP/reference	1.00104	0.885
41DAP/reference	0.98064	0.667
42DAP/reference	1.73399	0.001
43DAP/reference	1.67458	0.006
47DAP/reference	1.76963	0.001
52DAP/reference	1.00475	0.668
57DAP/reference	1.44989	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96336	0.679
27DAP/17DAP	1.03771	0.957
39DAP/27DAP	1.14247	0.383
41DAP/39DAP	1.08474	0.861
42DAP/41DAP	0.85863	0.296
43DAP/42DAP	0.90791	0.367
47DAP/43DAP	0.99837	0.989
52DAP/47DAP	1.15424	0.549
57DAP/52DAP	0.98129	0.789
57DAP/7DAP	0.92426	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76321	0.069
17DAP/reference	0.95287	0.389
27DAP/reference	1.19111	0.246
39DAP/reference	1.10791	0.252
41DAP/reference	1.02875	0.848
42DAP/reference	1.01187	0.751
43DAP/reference	0.94117	0.334
47DAP/reference	1.02962	0.98
52DAP/reference	0.98055	0.571
57DAP/reference	0.99667	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67047	0.007
17DAP/reference	0.65975	0.003
27DAP/reference	0.79323	0.097
39DAP/reference	0.64776	0.009
41DAP/reference	0.72799	0.024
42DAP/reference	0.69628	0.012
43DAP/reference	1.28165	0.509
47DAP/reference	0.84796	0.029
52DAP/reference	0.73339	0.005
57DAP/reference	0.8902	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80422	0.127
17DAP/reference	0.77273	0.109
27DAP/reference	1.44249	0.284
39DAP/reference	1.10327	1
41DAP/reference	0.91891	0.371
42DAP/reference	0.93833	0.445
43DAP/reference	1.18707	0.547
47DAP/reference	1.86954	0.005
52DAP/reference	1.28258	0.363
57DAP/reference	0.85204	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94141	1
26DAP/20DAP	1.18079	0.477
34DAP/26DAP	0.9048	0.741
51DAP/34DAP	1.15443	0.883
52DAP/51DAP	1.06692	0.808
53DAP/52DAP	1.23797	0.552
55DAP/53DAP	0.9621	0.735
57DAP/55DAP	1.24132	0.841
62DAP/57DAP	1.04482	1
68DAP/62DAP	0.88536	0.641
68DAP/14DAP	0.93003	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.5319	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67953	0.215
Mature Green Tomato/Ripe Tomato	0.37739	0.017
Immature Eggplant/Mature Eggplant	2.08027	0.116
Ripe Pepper/Ripe Tomato	0.46318	0.293
Mature Eggplant/Ripe Tomato	0.87485	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14866	0.742
1-1-2/M82	1.53304	1
12-2/M82	0.92414	0.955
12-4/M82	1.14781	1
1-3/M82	1.03788	1
2-1-1/M82	1.38326	0.295
2-1/M82	1.12201	1
2-6/M82	1.0817	0.695
3-2/M82	1.3113	0.463
4-1-1/M82	1.07646	1
4-1/M82	1.53148
4-3-2/M82	2.25976	0.241
4-3/M82	1.97172	0.268
5-3/M82	0.84353	0.419
6-2/M82	0.89982
6-3/M82	1.39979
7-1/M82	0.98432	1
7-2/M82	0.8671	1
9-3-2/M82	2.17724	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88511
IL2-6/WTpooled	2.05248	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08648	1
IL12-4/WTpooled	1.1993	1
IL1-4/WTpooled	1.05266	1
WT/WTpooled	1.01205	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	1.21662	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00974	1
DC3000/delta hrp 6h	3.76254
DC3000/delta hrp 12h	1.08656	1
DC3000/delta hrp 24h	1.00784	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.1967	0.693
Exp 60h	1.58111	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99562	1
Var 0h	0.9219	0.933
Var 12h I row2-row1	1.0882	0.613
Var 12h NI row2-row1	1.03265	1
Var 36h I row2-row1	0.9241	0.805
Var 36h NI row2-row1	0.84592	0.522
Var 60h I row2-row1	1.38812	1
Var 60h NI row2-row1	0.89399	1
Time course 0hI-0hNI	0.94052	0.408
Time course 12hI-12hNI	1.00234	1
Time course 36hI-36hNI	0.99573	0.753
Time course 60hI-60hNI	0.82861	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)	0.70103	0.309
transgenic ySAMdc/azygous control (breaker)	1.14247	0.248
transgenic ySAMdc/azygous control (red)	1.09844	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95679	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65763	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.91563	0.105
Manapal/WT (break)	1.01218	1
Manapal/WT (red)	1.08743	1