Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.20.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81264	0.331
27DAP/17DAP	1.06604	0.92
39DAP/27DAP	1.80742	0.159
41DAP/39DAP	1.15692	0.597
42DAP/41DAP	1.09195	1
43DAP/42DAP	1.09505	0.968
47DAP/43DAP	0.87926	0.603
52DAP/47DAP	0.911	0.734
57DAP/52DAP	0.94652	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83311	0.211
17DAP/reference	1.59583	0.427
27DAP/reference	0.98974	0.847
39DAP/reference	0.85852	0.024
41DAP/reference	0.802	0.341
42DAP/reference	1.02654
43DAP/reference	0.72095	0.36
47DAP/reference	0.42729	0.06
52DAP/reference	0.90885	0.36
57DAP/reference	0.73262	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96701	0.629
27DAP/17DAP	0.95789	0.748
39DAP/27DAP	1.05776	0.57
41DAP/39DAP	1.04458	0.896
42DAP/41DAP	1.04875	0.861
43DAP/42DAP	1.11756	0.162
47DAP/43DAP	1.04363	0.827
52DAP/47DAP	0.95179	0.797
57DAP/52DAP	0.94241	0.448
57DAP/7DAP	0.99613	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96008	0.445
17DAP/reference	0.72004	0.012
27DAP/reference	0.76945	0.017
39DAP/reference	0.96555	0.474
41DAP/reference	0.79061	0.044
42DAP/reference	0.8518	0.117
43DAP/reference	0.96802	0.334
47DAP/reference	1.40663	0.035
52DAP/reference	1.00764	0.571
57DAP/reference	0.67519	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07244	0.65
17DAP/reference	1.13763	0.151
27DAP/reference	1.11517	0.507
39DAP/reference	0.97932	0.509
41DAP/reference	0.95623	0.152
42DAP/reference	0.90999
43DAP/reference	0.96489	0.561
47DAP/reference	0.48904
52DAP/reference	0.87298	0.037
57DAP/reference	1.15013	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01938	1
17DAP/reference	0.82235	0.103
27DAP/reference	0.72832	0.036
39DAP/reference	0.83453	0.076
41DAP/reference	0.78968	0.05
42DAP/reference	0.8005	0.059
43DAP/reference	0.77679	0.023
47DAP/reference	0.93743	0.224
52DAP/reference	0.99713	0.573
57DAP/reference	0.9014	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20785	0.966
26DAP/20DAP	0.84978	0.512
34DAP/26DAP	0.99091	1
51DAP/34DAP	1.03468	0.84
52DAP/51DAP	1.02838	0.808
53DAP/52DAP	0.99062	0.96
55DAP/53DAP	1.138	0.748
57DAP/55DAP	1.13986	0.779
62DAP/57DAP	0.97352	0.994
68DAP/62DAP	1.16257	0.85
68DAP/14DAP	1.09522	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91877	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76806	0.245
Mature Green Tomato/Ripe Tomato	0.40117	0.017
Immature Eggplant/Mature Eggplant	1.32711	0.05
Ripe Pepper/Ripe Tomato	0.98221	1
Mature Eggplant/Ripe Tomato	0.62544	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00104	1
1-1-2/M82	0.85455	1
12-2/M82	1.13502	1
12-4/M82	0.93436	0.619
1-3/M82	0.87831	1
2-1-1/M82	1.06201	1
2-1/M82	0.95469
2-6/M82	1.12095	0.452
3-2/M82	0.84044	1
4-1-1/M82	0.96281	1
4-1/M82	0.97711
4-3-2/M82	0.91345	1
4-3/M82	0.80605	0.578
5-3/M82	0.88996	1
6-2/M82	0.93956	1
6-3/M82	0.99893	1
7-1/M82	0.87469
7-2/M82	1.05082	1
9-3-2/M82	0.98926	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31292
IL2-6/WTpooled	0.91522	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0712	1
IL12-4/WTpooled	0.85204	0.71
IL1-4/WTpooled	1.1947	1
WT/WTpooled	0.91473	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	1.01176	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98414	1
DC3000/delta hrp 6h	1.02159	0.95
DC3000/delta hrp 12h	1.02475	1
DC3000/delta hrp 24h	1.19128	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24836	0.087
DC3000 delta B/DC3000 delta AB	1.08267	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04446	1
Exp 36h	1.15753	0.489
Exp 60h	1.29249	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95525	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.15981	0.196
Var 12h NI row2-row1	0.91329	0.713
Var 36h I row2-row1	1.18698	0.908
Var 36h NI row2-row1	1.02872	1
Var 60h I row2-row1	0.91643	0.832
Var 60h NI row2-row1	1.21885	0.904
Time course 0hI-0hNI	1.01714	1
Time course 12hI-12hNI	1.17621	0.083
Time course 36hI-36hNI	1.22779	0.007
Time course 60hI-60hNI	1.98163	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)	0.96382	0.299
transgenic ySAMdc/azygous control (breaker)	1.28894	0.248
transgenic ySAMdc/azygous control (red)	1.11258	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28312	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86733	1
Manapal/WT (break)	0.99351	1
Manapal/WT (red)	0.61153	0.216