Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.13.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47954	0.365
27DAP/17DAP	0.89558	0.764
39DAP/27DAP	1.97123	0.458
41DAP/39DAP	0.98339	0.873
42DAP/41DAP	1.26374	0.691
43DAP/42DAP	1.00276	0.937
47DAP/43DAP	1.00026	0.92
52DAP/47DAP	0.86432	0.623
57DAP/52DAP	1.22413	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8333	0.027
17DAP/reference	0.98028	0.664
27DAP/reference	1.03618	0.559
39DAP/reference	0.96672	0.5
41DAP/reference	0.91022	0.114
42DAP/reference	0.85485	0.007
43DAP/reference	0.98558	0.728
47DAP/reference	0.92432	0.013
52DAP/reference	0.96306	0.382
57DAP/reference	0.95091	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62377	0.036
27DAP/17DAP	0.75546	0.363
39DAP/27DAP	1.23494	0.178
41DAP/39DAP	0.66927	0.019
42DAP/41DAP	1.15277	0.601
43DAP/42DAP	1.0154	0.83
47DAP/43DAP	0.82159	0.015
52DAP/47DAP	1.04825	0.826
57DAP/52DAP	0.78871	0.201
57DAP/7DAP	0.84272	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95768	0.402
17DAP/reference	0.83899	0.044
27DAP/reference	0.81859	0.024
39DAP/reference	1.14402	0.282
41DAP/reference	0.81477	0.038
42DAP/reference	1.05891	1
43DAP/reference	1.35733	0.226
47DAP/reference	1.1149	0.632
52DAP/reference	0.9984	0.621
57DAP/reference	1.03724	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87993	0.157
17DAP/reference	0.81303	0.005
27DAP/reference	0.82643	0.03
39DAP/reference	0.87391	0.152
41DAP/reference	0.82083	0.024
42DAP/reference	0.81038	0.042
43DAP/reference	0.83879	0.082
47DAP/reference	0.85839	0.021
52DAP/reference	0.88614	0.047
57DAP/reference	0.88434	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91757	0.311
17DAP/reference	0.90338	0.381
27DAP/reference	0.93194	0.27
39DAP/reference	0.96492	0.43
41DAP/reference	0.94948	0.417
42DAP/reference	1.19307	0.391
43DAP/reference	1.10919	0.768
47DAP/reference	0.98291	0.538
52DAP/reference	0.96831	0.65
57DAP/reference	0.62458	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06681	0.966
26DAP/20DAP	1.01234	1
34DAP/26DAP	1.19545	0.819
51DAP/34DAP	1.22862	0.581
52DAP/51DAP	0.81503	1
53DAP/52DAP	0.70386	0.316
55DAP/53DAP	0.72483	0.135
57DAP/55DAP	1.31782	0.256
62DAP/57DAP	0.89946	0.871
68DAP/62DAP	1.0338	0.984
68DAP/14DAP	0.63141	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94196	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.09286	0.058
Mature Green Tomato/Ripe Tomato	2.18383	0.044
Immature Eggplant/Mature Eggplant	1.58464
Ripe Pepper/Ripe Tomato	1.01272	1
Mature Eggplant/Ripe Tomato	0.67626	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.68918	0.5
1-1-2/M82	1.04587	1
12-2/M82	1.04882	1
12-4/M82	0.78141
1-3/M82	N/A	N/A
2-1-1/M82	0.87067
2-1/M82	0.98785	0.322
2-6/M82	1.42163	0.374
3-2/M82	0.93197	1
4-1-1/M82	1.12472	1
4-1/M82	N/A	N/A
4-3-2/M82	1.43173
4-3/M82	1.52242
5-3/M82	0.98522	1
6-2/M82	2.15181
6-3/M82	1.02204	1
7-1/M82	0.86582	1
7-2/M82	N/A	N/A
9-3-2/M82	1.2017	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.84012	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09318	0.362
IL12-4/WTpooled	0.88619	0.581
IL1-4/WTpooled	1.09836
WT/WTpooled	0.92904	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	1.052	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91722	1
DC3000/delta hrp 6h	1.17155	1
DC3000/delta hrp 12h	0.89261	1
DC3000/delta hrp 24h	0.61933	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5852
DC3000 delta B/DC3000 delta AB	0.64755	0.028

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9361	1
Exp 36h	0.78973	0.623
Exp 60h	0.81373	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99653	1
Var 0h	1.04796	0.421
Var 12h I row2-row1	0.82898	0.344
Var 12h NI row2-row1	0.92899	0.713
Var 36h I row2-row1	0.83333	1
Var 36h NI row2-row1	1.3346	0.482
Var 60h I row2-row1	0.79413	0.287
Var 60h NI row2-row1	1.14716	0.904
Time course 0hI-0hNI	0.98986	1
Time course 12hI-12hNI	0.94447	0.495
Time course 36hI-36hNI	0.84971	0.064
Time course 60hI-60hNI	0.41815	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)	0.92177	0.314
transgenic ySAMdc/azygous control (breaker)	1.55632	0.248
transgenic ySAMdc/azygous control (red)	1.11335	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99941	0.911

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16216	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.82609	0.084
Manapal/WT (break)	2.62902	0.123
Manapal/WT (red)	1.83355	0.15