Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.4.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89629	0.405
27DAP/17DAP	0.92453	0.827
39DAP/27DAP	1.10015	0.864
41DAP/39DAP	0.87795	0.524
42DAP/41DAP	1.15787	0.755
43DAP/42DAP	1.08624	1
47DAP/43DAP	0.87797	0.595
52DAP/47DAP	1.27738	0.721
57DAP/52DAP	1.21184	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85612	0.075
17DAP/reference	0.82774	0.147
27DAP/reference	0.84283	0.054
39DAP/reference	0.85632	0.234
41DAP/reference	0.79247	0.114
42DAP/reference	0.86608	0.008
43DAP/reference	0.88308	0.107
47DAP/reference	0.95084	0.191
52DAP/reference	0.88699	0.121
57DAP/reference	0.90053	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54398	0.036
27DAP/17DAP	1.36605	0.077
39DAP/27DAP	0.85389	0.456
41DAP/39DAP	0.82699	0.446
42DAP/41DAP	1.334	0.042
43DAP/42DAP	1.04932	0.699
47DAP/43DAP	0.9897	0.902
52DAP/47DAP	0.95228	0.876
57DAP/52DAP	1.17303	0.346
57DAP/7DAP	0.47861	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89688	0.086
17DAP/reference	0.95292	0.295
27DAP/reference	0.91071	0.101
39DAP/reference	0.89675	0.146
41DAP/reference	0.80321	0.056
42DAP/reference	0.79543	0.073
43DAP/reference	0.7684	0.022
47DAP/reference	0.90933	0.128
52DAP/reference	0.76739	0.012
57DAP/reference	0.88523	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89527	0.353
17DAP/reference	0.7962	0.009
27DAP/reference	0.97532	0.519
39DAP/reference	0.91586	0.095
41DAP/reference	0.92161	0.081
42DAP/reference	0.80322	0.012
43DAP/reference	1.03287	0.846
47DAP/reference	0.85253	0.043
52DAP/reference	0.90425	0.121
57DAP/reference	0.99979	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21631	0.093
17DAP/reference	0.95294	0.389
27DAP/reference	0.83816	0.048
39DAP/reference	0.95437	0.393
41DAP/reference	0.93341	0.371
42DAP/reference	0.83868	0.036
43DAP/reference	0.92106	0.171
47DAP/reference	0.97949	0.525
52DAP/reference	1.37725	0.509
57DAP/reference	0.8026	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21717	0.966
26DAP/20DAP	0.95243	1
34DAP/26DAP	0.89374	0.861
51DAP/34DAP	1.17133	0.909
52DAP/51DAP	1.06379	0.954
53DAP/52DAP	0.9462	0.767
55DAP/53DAP	1.17748	0.898
57DAP/55DAP	0.91491	0.629
62DAP/57DAP	0.95093	0.871
68DAP/62DAP	0.72273	0.101
68DAP/14DAP	0.92912	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83874	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70129	0.226
Mature Green Tomato/Ripe Tomato	1.47566	0.02
Immature Eggplant/Mature Eggplant	1.17005	N/A
Ripe Pepper/Ripe Tomato	1.1648	1
Mature Eggplant/Ripe Tomato	1.18094	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80808	N/A
1-1-2/M82	0.9625	1
12-2/M82	0.72278	N/A
12-4/M82	1.06717	N/A
1-3/M82	1.48202	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.00823	1
3-2/M82	1.45287	0.463
4-1-1/M82	0.97557	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.26565	0.241
4-3/M82	1.19497	0.268
5-3/M82	1.18024	0.467
6-2/M82	1.12461	N/A
6-3/M82	1.0393	1
7-1/M82	1.38073	0.547
7-2/M82	N/A	N/A
9-3-2/M82	1.11151	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.0896	0.46
IL7-5/WTpooled	1.60177	N/A
IL7-3/WTpooled	1.12078	0.362
IL12-4/WTpooled	1.10233	0.839
IL1-4/WTpooled	0.86847	0.415
WT/WTpooled	1.00307	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	1.04857	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05972	0.921
DC3000/delta hrp 6h	1.01475	0.95
DC3000/delta hrp 12h	0.80602	1
DC3000/delta hrp 24h	1.01189	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.33634	0.023
DC3000 delta B/DC3000 delta AB	0.47112	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9863	1
Var 0h	1.10827	0.98
Var 12h I row2-row1	0.89929	0.338
Var 12h NI row2-row1	0.7605	0.36
Var 36h I row2-row1	0.79493	1
Var 36h NI row2-row1	1.22617	0.482
Var 60h I row2-row1	1.28894	1
Var 60h NI row2-row1	1.27068	0.904
Time course 0hI-0hNI	0.85638	0.063
Time course 12hI-12hNI	1.03118	0.811
Time course 36hI-36hNI	0.85035	0.027
Time course 60hI-60hNI	0.1816	0.005

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)	0.94641	0.213
transgenic ySAMdc/azygous control (breaker)	1.08851	0.248
transgenic ySAMdc/azygous control (red)	1.07873	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06232	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01701	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87848	0.172
Manapal/WT (break)	0.80156	0.333
Manapal/WT (red)	0.97941	0.863