Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.7.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.59001	0.048
27DAP/17DAP	0.52428	0.042
39DAP/27DAP	0.82135	0.512
41DAP/39DAP	0.79125	0.333
42DAP/41DAP	0.96772	1
43DAP/42DAP	1.37378	0.569
47DAP/43DAP	0.96139	0.788
52DAP/47DAP	1.18953	0.784
57DAP/52DAP	1.08444	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62743	0.071
17DAP/reference	0.92655	0.208
27DAP/reference	0.9792	0.654
39DAP/reference	0.7168	0.031
41DAP/reference	0.76076	0.026
42DAP/reference	0.87378	0.002
43DAP/reference	0.89303	0.247
47DAP/reference	0.76553	0.003
52DAP/reference	0.73426	0.089
57DAP/reference	0.90865	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37325	0.032
27DAP/17DAP	2.09638	0.044
39DAP/27DAP	0.55181	0.058
41DAP/39DAP	0.46452	0.013
42DAP/41DAP	0.88523	0.439
43DAP/42DAP	1.1019	0.664
47DAP/43DAP	0.91223	0.63
52DAP/47DAP	0.96566	0.905
57DAP/52DAP	0.90075	0.501
57DAP/7DAP	0.56169	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93891	0.296
17DAP/reference	0.63506	0.012
27DAP/reference	0.46327	0.01
39DAP/reference	0.438	0.011
41DAP/reference	0.45391	0.011
42DAP/reference	0.5683	0.015
43DAP/reference	0.50994	0.01
47DAP/reference	0.51708	0.03
52DAP/reference	0.43024	0.011
57DAP/reference	0.49318	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.216	0.926
17DAP/reference	1.36181	0.191
27DAP/reference	1.3127	0.143
39DAP/reference	0.80516	0.097
41DAP/reference	0.86512	0.081
42DAP/reference	0.82773	0.169
43DAP/reference	0.76398	0.147
47DAP/reference	0.75743	0.021
52DAP/reference	0.63384	0.006
57DAP/reference	0.66747	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28819	0.037
17DAP/reference	1.16603	0.551
27DAP/reference	0.79374	0.062
39DAP/reference	0.70377	0.019
41DAP/reference	0.41613	0.018
42DAP/reference	0.56517	0.032
43DAP/reference	0.54808	0.035
47DAP/reference	0.67073	0.006
52DAP/reference	0.46462	0.06
57DAP/reference	0.81301	0.12

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12888	0.966
26DAP/20DAP	1.22366	0.813
34DAP/26DAP	0.71038	0.177
51DAP/34DAP	0.65095	0.065
52DAP/51DAP	1.02647	0.742
53DAP/52DAP	0.81343	0.049
55DAP/53DAP	0.65307	0.029
57DAP/55DAP	0.65682	0.14
62DAP/57DAP	1.05467	1
68DAP/62DAP	1.4092	0.162
68DAP/14DAP	0.38366	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.17657	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.54804	0.058
Mature Green Tomato/Ripe Tomato	38.5764	0.025
Immature Eggplant/Mature Eggplant	0.2982	0.057
Ripe Pepper/Ripe Tomato	42.7089	0.251
Mature Eggplant/Ripe Tomato	73.604	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.82876	0.619
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	1.28032
3-2/M82	0.93347
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.98203
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10402	0.277
IL2-6/WTpooled	0.66506	0.473
IL7-5/WTpooled	0.7675	1
IL7-3/WTpooled	1.40353	1
IL12-4/WTpooled	0.89775	0.71
IL1-4/WTpooled	0.78915	0.834
WT/WTpooled	1.0511	0.85

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	0.81696	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95003	1
DC3000/delta hrp 6h	0.87727	0.95
DC3000/delta hrp 12h	0.79142	1
DC3000/delta hrp 24h	0.31409	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.43627	0.023
DC3000 delta B/DC3000 delta AB	0.46068	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91162	1
Exp 36h	0.72154	0.539
Exp 60h	0.55552	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00045	1
Var 0h	1.03255	0.98
Var 12h I row2-row1	0.95015	0.856
Var 12h NI row2-row1	0.89891	0.713
Var 36h I row2-row1	1.05565	0.908
Var 36h NI row2-row1	1.24488	1
Var 60h I row2-row1	1.13707	0.562
Var 60h NI row2-row1	1.01824	1
Time course 0hI-0hNI	1.04748	0.852
Time course 12hI-12hNI	0.97411	0.847
Time course 36hI-36hNI	0.80663	0.023
Time course 60hI-60hNI	0.14474	0.005

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)	0.76898	0.348
transgenic ySAMdc/azygous control (breaker)	1.59612	1
transgenic ySAMdc/azygous control (red)	0.97904	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.67262	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.76723	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.66243	0.096
Manapal/WT (break)	1.95548	1
Manapal/WT (red)	0.94775	0.728