Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.3.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90822	0.445
27DAP/17DAP	0.8934	0.753
39DAP/27DAP	1.117	0.841
41DAP/39DAP	0.96643	0.852
42DAP/41DAP	1.08366	0.882
43DAP/42DAP	0.91285	0.829
47DAP/43DAP	0.92608	0.724
52DAP/47DAP	1.10462	0.973
57DAP/52DAP	1.03448	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03136	0.928
17DAP/reference	0.99732	0.957
27DAP/reference	0.94706	0.385
39DAP/reference	1.07111	0.514
41DAP/reference	0.9496	0.434
42DAP/reference	0.99417	0.547
43DAP/reference	1.00145	0.942
47DAP/reference	0.95774	0.137
52DAP/reference	0.87113	0.062
57DAP/reference	0.89907	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02246	0.858
27DAP/17DAP	1.0045	1
39DAP/27DAP	1.00976	0.799
41DAP/39DAP	1.03305	0.807
42DAP/41DAP	1.01985	0.916
43DAP/42DAP	0.97929	0.684
47DAP/43DAP	0.97339	0.796
52DAP/47DAP	0.98615	0.925
57DAP/52DAP	1.00315	1
57DAP/7DAP	1.01547	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03776	0.638
17DAP/reference	0.98791	0.518
27DAP/reference	0.96991	0.248
39DAP/reference	1.02688	0.538
41DAP/reference	0.9738	0.357
42DAP/reference	0.90779	0.02
43DAP/reference	0.92018	0.22
47DAP/reference	0.99054	0.671
52DAP/reference	0.99111	0.679
57DAP/reference	0.99452	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03044	0.679
17DAP/reference	0.99346	0.548
27DAP/reference	1.05262	0.86
39DAP/reference	0.99118	0.586
41DAP/reference	0.92257	0.056
42DAP/reference	0.95336	0.212
43DAP/reference	0.96535	0.45
47DAP/reference	0.94815	0.061
52DAP/reference	0.96512	0.171
57DAP/reference	0.90543	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06804	0.244
17DAP/reference	0.98721	0.751
27DAP/reference	0.94058	0.038
39DAP/reference	1.0332	0.546
41DAP/reference	1.00688	1
42DAP/reference	0.92085	0.22
43DAP/reference	0.95032	0.15
47DAP/reference	1.00989	1
52DAP/reference	1.00035	0.946
57DAP/reference	0.87211	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96909	1
26DAP/20DAP	0.99874	1
34DAP/26DAP	1.0019	1
51DAP/34DAP	1.01764	0.795
52DAP/51DAP	0.97893	1
53DAP/52DAP	1.04248	0.882
55DAP/53DAP	0.95837	0.725
57DAP/55DAP	0.83587	0.452
62DAP/57DAP	0.96585	N/A
68DAP/62DAP	1.02978	0.834
68DAP/14DAP	1.19465	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02503	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97772	0.783
Mature Green Tomato/Ripe Tomato	1.25789	N/A
Immature Eggplant/Mature Eggplant	1.13543	0.058
Ripe Pepper/Ripe Tomato	1.18303	1
Mature Eggplant/Ripe Tomato	1.21261	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89619	0.69
1-1-2/M82	0.83087	1
12-2/M82	0.91001	0.535
12-4/M82	1.09265	1
1-3/M82	1.0604	1
2-1-1/M82	0.96715	1
2-1/M82	0.9975	1
2-6/M82	0.89025	1
3-2/M82	1.02715	0.967
4-1-1/M82	1.02334	1
4-1/M82	0.8932	1
4-3-2/M82	1.01799	0.508
4-3/M82	0.94635	0.72
5-3/M82	0.94602	0.642
6-2/M82	0.99865	1
6-3/M82	0.96488	1
7-1/M82	0.98223	1
7-2/M82	0.8705	0.599
9-3-2/M82	1.4379	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.95274	N/A
IL2-6/WTpooled	0.61727	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.44351	0.362
IL12-4/WTpooled	1.21725	0.737
IL1-4/WTpooled	1.0683	1
WT/WTpooled	1.02982	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	1.21591	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01703	0.921
DC3000/delta hrp 6h	0.95081	0.95
DC3000/delta hrp 12h	1.01697	1
DC3000/delta hrp 24h	1.04451	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16305	0.333
DC3000 delta B/DC3000 delta AB	1.01216	0.738

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82448	1
Exp 36h	1.19912	0.693
Exp 60h	0.95938	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97868	1
Var 0h	0.48376	1
Var 12h I row2-row1	1.27225	0.198
Var 12h NI row2-row1	1.06546	0.34
Var 36h I row2-row1	0.86217	0.805
Var 36h NI row2-row1	0.90623	0.478
Var 60h I row2-row1	1.04147	1
Var 60h NI row2-row1	1.03213	1
Time course 0hI-0hNI	1.02232	1
Time course 12hI-12hNI	1.06437	0.734
Time course 36hI-36hNI	1.20229	0.07
Time course 60hI-60hNI	1.92804	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)	1.00304	1
transgenic ySAMdc/azygous control (breaker)	1.51509	0.248
transgenic ySAMdc/azygous control (red)	1.20941	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04415	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93315	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93368	1
Manapal/WT (break)	1.09678	1
Manapal/WT (red)	0.93127	0.607