Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09108	0.838
27DAP/17DAP	0.96041	0.947
39DAP/27DAP	1.17805	0.643
41DAP/39DAP	1.09059	0.871
42DAP/41DAP	1.05575	0.967
43DAP/42DAP	1.7678	0.069
47DAP/43DAP	0.84479	0.51
52DAP/47DAP	1.41462	0.506
57DAP/52DAP	0.92297	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02709	0.693
17DAP/reference	0.99342	0.904
27DAP/reference	1.4262	0.446
39DAP/reference	0.97029	0.72
41DAP/reference	1.2038	0.187
42DAP/reference	0.98296	0.484
43DAP/reference	N/A	N/A
47DAP/reference	1.05354	0.148
52DAP/reference	0.91415	0.292
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91173	0.629
27DAP/17DAP	0.90997	0.58
39DAP/27DAP	1.00534	1
41DAP/39DAP	1.01833	1
42DAP/41DAP	1.06353	1
43DAP/42DAP	1.06539	0.513
47DAP/43DAP	0.98115	0.911
52DAP/47DAP	0.97388	0.902
57DAP/52DAP	0.98692	0.828
57DAP/7DAP	0.7897	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.21663	0.026
17DAP/reference	3.53727	0.006
27DAP/reference	2.57685	0.006
39DAP/reference	3.21838	0.005
41DAP/reference	3.07082	0.01
42DAP/reference	3.39416	0.006
43DAP/reference	4.44647	0.007
47DAP/reference	2.48324	0.075
52DAP/reference	3.08915	0.007
57DAP/reference	2.70994	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05741	0.724
17DAP/reference	1.11457	0.107
27DAP/reference	1.05367	0.607
39DAP/reference	1.01149	1
41DAP/reference	1.03232	0.91
42DAP/reference	0.95575	0.289
43DAP/reference	0.87105	0.32
47DAP/reference	0.96684	0.5
52DAP/reference	1.02626	0.838
57DAP/reference	1.07059	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.39618	0.025
17DAP/reference	1.58835	0.398
27DAP/reference	3.65188	0.02
39DAP/reference	3.1702	0.009
41DAP/reference	3.16317	0.007
42DAP/reference	3.13701	0.009
43DAP/reference	4.02441	0.006
47DAP/reference	1.03231	0.655
52DAP/reference	3.535	0.054
57DAP/reference	2.82621	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90739	0.807
26DAP/20DAP	0.99868	1
34DAP/26DAP	1.00918	1
51DAP/34DAP	1.09993	0.339
52DAP/51DAP	0.99918	1
53DAP/52DAP	1.00197	1
55DAP/53DAP	0.90962	0.115
57DAP/55DAP	1.37992	0.214
62DAP/57DAP	1.00154	1
68DAP/62DAP	1.13129	0.398
68DAP/14DAP	1.07939	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9149	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70789	0.23
Mature Green Tomato/Ripe Tomato	0.50876	0.031
Immature Eggplant/Mature Eggplant	1.66973	0.053
Ripe Pepper/Ripe Tomato	0.75154	1
Mature Eggplant/Ripe Tomato	0.67951	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95398
1-1-2/M82	0.92049
12-2/M82	N/A	N/A
12-4/M82	0.91542	0.358
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	N/A	N/A
3-2/M82	N/A	N/A
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	0.94502
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	0.89645	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.02837	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.89981	0.394
WT/WTpooled	N/A	N/A

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	1.15244	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05826	0.921
DC3000/delta hrp 6h	0.94537	0.95
DC3000/delta hrp 12h	1.13056	1
DC3000/delta hrp 24h	1.25794	0.192

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.33366	0.145
DC3000 delta B/DC3000 delta AB	1.05087	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0417	1
Exp 36h	1.37528	0.693
Exp 60h	1.47009	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99964	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10918	0.196
Var 12h NI row2-row1	0.88784	0.546
Var 36h I row2-row1	0.93664	1
Var 36h NI row2-row1	0.94912	0.791
Var 60h I row2-row1	0.95228	0.952
Var 60h NI row2-row1	1.06815	1
Time course 0hI-0hNI	1.1033	0.799
Time course 12hI-12hNI	1.03998	0.703
Time course 36hI-36hNI	1.10529	0.401
Time course 60hI-60hNI	1.47656	0.008

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)	1.03105	0.482
transgenic ySAMdc/azygous control (breaker)	0.96933	1
transgenic ySAMdc/azygous control (red)	0.93373	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97836	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0536	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09885	0.307
Manapal/WT (break)	0.98166	1
Manapal/WT (red)	1.2913	0.413