Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.11.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75894	0.162
27DAP/17DAP	0.99754	1
39DAP/27DAP	0.86483	0.512
41DAP/39DAP	1.00385	0.929
42DAP/41DAP	1.09428	0.926
43DAP/42DAP	0.98238	0.925
47DAP/43DAP	1.0592	0.95
52DAP/47DAP	0.97211	0.848
57DAP/52DAP	0.90447	0.778

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08897	0.403
17DAP/reference	0.90563	0.069
27DAP/reference	0.92878	0.059
39DAP/reference	0.87343	0.132
41DAP/reference	0.85432	0.065
42DAP/reference	0.88746	0.001
43DAP/reference	0.94346	0.429
47DAP/reference	0.85219	0.013
52DAP/reference	0.82931	0.026
57DAP/reference	0.79986	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02558	0.871
27DAP/17DAP	0.91959	0.339
39DAP/27DAP	1.0014	1
41DAP/39DAP	1.0857	0.484
42DAP/41DAP	0.91975	0.425
43DAP/42DAP	0.85072	0.036
47DAP/43DAP	1.07405	0.593
52DAP/47DAP	0.98215	0.913
57DAP/52DAP	0.92156	0.505
57DAP/7DAP	1.02826	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96965	0.024
17DAP/reference	1.78373	0.007
27DAP/reference	1.45868	0.018
39DAP/reference	1.84071	0.008
41DAP/reference	1.45202	0.029
42DAP/reference	1.55271	0.03
43DAP/reference	1.74719	0.009
47DAP/reference	1.12215	1
52DAP/reference	1.93453	0.009
57DAP/reference	1.62081	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15559	0.43
17DAP/reference	0.83437	0.072
27DAP/reference	0.95312	0.407
39DAP/reference	0.7631	0.01
41DAP/reference	0.77172	0.032
42DAP/reference	0.83637	0.032
43DAP/reference	0.68574	0.022
47DAP/reference	0.91051	0.064
52DAP/reference	0.74491	0.004
57DAP/reference	0.77689	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25243	0.158
17DAP/reference	1.24751	0.638
27DAP/reference	1.78675	0.034
39DAP/reference	1.52252	0.035
41DAP/reference	1.43716	0.104
42DAP/reference	1.30382	0.34
43DAP/reference	1.22777	0.84
47DAP/reference	0.76731	0.009
52DAP/reference	1.4246	0.384
57DAP/reference	0.78124	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95726	1
26DAP/20DAP	1.12431	0.598
34DAP/26DAP	1.03112	1
51DAP/34DAP	1.32327	0.067
52DAP/51DAP	0.85572	1
53DAP/52DAP	1.02424	0.91
55DAP/53DAP	0.94597	0.675
57DAP/55DAP	1.08902	0.71
62DAP/57DAP	0.9561	0.871
68DAP/62DAP	0.97208	0.81
68DAP/14DAP	1.02797	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02923	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48842	0.107
Mature Green Tomato/Ripe Tomato	1.62371	0.106
Immature Eggplant/Mature Eggplant	1.84223	0.05
Ripe Pepper/Ripe Tomato	1.6677	0.258
Mature Eggplant/Ripe Tomato	0.85733	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96669	0.944
1-1-2/M82	1.12583	1
12-2/M82	1.0823	1
12-4/M82	0.94737	0.358
1-3/M82	0.97876	1
2-1-1/M82	1.02884
2-1/M82	N/A	N/A
2-6/M82	0.99331	1
3-2/M82	N/A	N/A
4-1-1/M82	0.97189	1
4-1/M82	1.18517	0.853
4-3-2/M82	1.05141
4-3/M82	1.0661	1
5-3/M82	1.04473	1
6-2/M82	1.00003	1
6-3/M82	0.93678	1
7-1/M82	N/A	N/A
7-2/M82	1.16193	1
9-3-2/M82	1.25924	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.85772	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07754	1
IL12-4/WTpooled	1.01512	0.839
IL1-4/WTpooled	1.01419
WT/WTpooled	1.01298	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	0.92687	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94025	1
DC3000/delta hrp 6h	1.03173	0.95
DC3000/delta hrp 12h	0.9634	1
DC3000/delta hrp 24h	0.96443	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98942	1
DC3000 delta B/DC3000 delta AB	1.01044	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06029	1
Exp 36h	0.90789	0.749
Exp 60h	1.02794	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97038	1
Var 0h	1.24093	0.594
Var 12h I row2-row1	0.89183	0.338
Var 12h NI row2-row1	0.98895	1
Var 36h I row2-row1	0.92375	1
Var 36h NI row2-row1	1.85404	1
Var 60h I row2-row1	0.84345	0.374
Var 60h NI row2-row1	0.93383	1
Time course 0hI-0hNI	1.02342	1
Time course 12hI-12hNI	0.98099	0.886
Time course 36hI-36hNI	1.15996	0.218
Time course 60hI-60hNI	0.88345	0.161

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)	0.85928	0.314
transgenic ySAMdc/azygous control (breaker)	1.06961	1
transgenic ySAMdc/azygous control (red)	1.23948	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99136	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02885	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.91846	0.086
Manapal/WT (break)	1.91887	0.183
Manapal/WT (red)	1.78272	0.142