Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70777	0.134
27DAP/17DAP	1.75539	0.902
39DAP/27DAP	1.25343	0.713
41DAP/39DAP	1.42864	0.252
42DAP/41DAP	0.92383	1
43DAP/42DAP	1.16289	1
47DAP/43DAP	0.92868	0.671
52DAP/47DAP	0.83212	0.615
57DAP/52DAP	0.83346	0.431

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81853	0.074
17DAP/reference	1.13449	0.178
27DAP/reference	1.1915	0.115
39DAP/reference	1.09981	0.413
41DAP/reference	1.06534	0.587
42DAP/reference	0.94764	0.169
43DAP/reference	1.07029	0.202
47DAP/reference	0.94025	0.137
52DAP/reference	0.94741	0.33
57DAP/reference	0.89425	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17986	0.662
27DAP/17DAP	1.24788	0.488
39DAP/27DAP	0.86642	0.388
41DAP/39DAP	1.05966	0.88
42DAP/41DAP	0.8814	0.343
43DAP/42DAP	1.02129	0.788
47DAP/43DAP	0.92568	0.617
52DAP/47DAP	1.38574	0.57
57DAP/52DAP	0.78285	0.405
57DAP/7DAP	1.24134	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48507	0.038
17DAP/reference	1.63598	0.008
27DAP/reference	1.17561	0.073
39DAP/reference	1.52607	0.007
41DAP/reference	1.42795	0.026
42DAP/reference	1.64657	0.008
43DAP/reference	1.43743	0.022
47DAP/reference	1.15496	0.353
52DAP/reference	1.14824	0.428
57DAP/reference	1.24353	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03647	0.926
17DAP/reference	0.98424	0.626
27DAP/reference	0.8483	0.076
39DAP/reference	0.93375	0.348
41DAP/reference	0.93792	0.34
42DAP/reference	0.9047	0.169
43DAP/reference	0.96374	0.516
47DAP/reference	1.3083	0.572
52DAP/reference	0.9584	0.351
57DAP/reference	0.97691	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31171	0.035
17DAP/reference	1.05104	0.824
27DAP/reference	1.46928	0.035
39DAP/reference	1.29496	0.026
41DAP/reference	1.08353	0.319
42DAP/reference	1.0098	1
43DAP/reference	0.95504	0.468
47DAP/reference	0.9265	0.269
52DAP/reference	1.29305	0.085
57DAP/reference	0.86663	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02646	1
26DAP/20DAP	0.73886	1
34DAP/26DAP	1.06538	1
51DAP/34DAP	1.37397	0.033
52DAP/51DAP	1.20449	0.776
53DAP/52DAP	0.946	0.807
55DAP/53DAP	1.05759	0.927
57DAP/55DAP	0.94906	0.872
62DAP/57DAP	1.06485	0.868
68DAP/62DAP	1.03541	0.885
68DAP/14DAP	0.72559	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92858	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26784	0.113
Mature Green Tomato/Ripe Tomato	1.72958	0.028
Immature Eggplant/Mature Eggplant	0.71523	N/A
Ripe Pepper/Ripe Tomato	9.53113	0.256
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
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	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	1.09505	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97196	1
IL12-4/WTpooled	1.31484	0.516
IL1-4/WTpooled	0.80809	0.834
WT/WTpooled	1.04764	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	1.07527	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11829	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.21572	1
DC3000/delta hrp 24h	1.2603	0.232

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09405	0.384
DC3000 delta B/DC3000 delta AB	1.15063	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78922	1
Exp 36h	2.18047	1
Exp 60h	1.45232	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9785	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.17277	0.544
Var 12h NI row2-row1	1.43982	0.649
Var 36h I row2-row1	0.97569	1
Var 36h NI row2-row1	0.75996	0.478
Var 60h I row2-row1	0.77798	0.832
Var 60h NI row2-row1	1.02924	1
Time course 0hI-0hNI	1.05327	0.799
Time course 12hI-12hNI	1.13758	0.07
Time course 36hI-36hNI	1.25321	0.008
Time course 60hI-60hNI	1.29224	0.01

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)	1.17645	0.347
transgenic ySAMdc/azygous control (breaker)	1.15224	0.248
transgenic ySAMdc/azygous control (red)	0.99349	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10255	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84935	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8438	1
Manapal/WT (break)	1.03863	1
Manapal/WT (red)	0.85034	0.274