Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04554	0.878
27DAP/17DAP	1.24846	0.8
39DAP/27DAP	0.90074	0.594
41DAP/39DAP	2.10025	0.264
42DAP/41DAP	1.04448	1
43DAP/42DAP	0.927	0.813
47DAP/43DAP	1.24881	0.659
52DAP/47DAP	1.23616	0.654
57DAP/52DAP	1.05	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98705	0.661
17DAP/reference	0.83999	0.026
27DAP/reference	1.03976	0.831
39DAP/reference	0.89023	0.276
41DAP/reference	0.85665	0.026
42DAP/reference	1.02766	0.414
43DAP/reference	0.94235	0.211
47DAP/reference	0.9799	0.345
52DAP/reference	1.38136	0.016
57DAP/reference	1.18993	0.037

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94717	0.542
27DAP/17DAP	1.01611	1
39DAP/27DAP	0.98544	0.943
41DAP/39DAP	0.99369	1
42DAP/41DAP	1.04713	0.81
43DAP/42DAP	1.05591	0.513
47DAP/43DAP	1.1015	0.708
52DAP/47DAP	0.98564	0.93
57DAP/52DAP	0.89674	0.169
57DAP/7DAP	1.14634	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92885	0.074
17DAP/reference	1.00852	0.971
27DAP/reference	1.01297	0.664
39DAP/reference	0.91499	0.012
41DAP/reference	0.85223	0.018
42DAP/reference	0.83151	0.01
43DAP/reference	0.87979	0.037
47DAP/reference	0.93728	0.504
52DAP/reference	0.88186	0.115
57DAP/reference	0.86994	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98763	0.811
17DAP/reference	1.01054	0.898
27DAP/reference	0.99346	0.642
39DAP/reference	0.96975	0.442
41DAP/reference	1.01672	1
42DAP/reference	0.98367	0.534
43DAP/reference	1.00271	0.846
47DAP/reference	0.93742	0.087
52DAP/reference	1.02371	0.471
57DAP/reference	0.81833	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0063	1
17DAP/reference	0.95214	0.636
27DAP/reference	1.18419	0.373
39DAP/reference	1.01155	0.792
41DAP/reference	1.01742	0.734
42DAP/reference	1.14241	0.356
43DAP/reference	1.14562	0.241
47DAP/reference	0.96874	0.646
52DAP/reference	1.00005	0.946
57DAP/reference	1.69299	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00939	1
26DAP/20DAP	1.02446	1
34DAP/26DAP	0.93499	0.771
51DAP/34DAP	0.95776	0.688
52DAP/51DAP	1.01773	0.925
53DAP/52DAP	1.1411	0.502
55DAP/53DAP	0.92	0.218
57DAP/55DAP	0.98315	0.872
62DAP/57DAP	1.04878	0.723
68DAP/62DAP	1.09571	0.945
68DAP/14DAP	0.98136	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05619	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52644
Mature Green Tomato/Ripe Tomato	1.28617	0.119
Immature Eggplant/Mature Eggplant	1.01593	0.606
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9831	0.961
1-1-2/M82	0.75388
12-2/M82	1.11816
12-4/M82	1.01707	1
1-3/M82	0.94773	0.501
2-1-1/M82	1.12617	0.689
2-1/M82	N/A	N/A
2-6/M82	1.00024	1
3-2/M82	0.97942
4-1-1/M82	1.01807	1
4-1/M82	2.04484	0.853
4-3-2/M82	0.81274	0.698
4-3/M82	0.96945	1
5-3/M82	1.01413	1
6-2/M82	1.00889	1
6-3/M82	1.02003	1
7-1/M82	1.22809
7-2/M82	0.97784	1
9-3-2/M82	0.76127	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.73661	0.566
IL1-4/WTpooled	0.97254	1
WT/WTpooled	1.11238	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	0.7909	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98052	1
DC3000/delta hrp 6h	0.96351	0.95
DC3000/delta hrp 12h	1.04759	1
DC3000/delta hrp 24h	1.10737	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0463	0.515
DC3000 delta B/DC3000 delta AB	1.04544	0.539

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	0.98257	1
Var 0h	0.77935	0.261
Var 12h I row2-row1	1.604	0.443
Var 12h NI row2-row1	1.08008	1
Var 36h I row2-row1	1.07071	1
Var 36h NI row2-row1	0.85995	0.61
Var 60h I row2-row1	1.50123	0.562
Var 60h NI row2-row1	1.18386	0.904
Time course 0hI-0hNI	1.01642	1
Time course 12hI-12hNI	1.00518	1
Time course 36hI-36hNI	0.94406	0.15
Time course 60hI-60hNI	1.09699	0.16

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)	1.05952	0.541
transgenic ySAMdc/azygous control (breaker)	0.88204	0.139
transgenic ySAMdc/azygous control (red)	0.99194	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03649	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00759	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77353	1
Manapal/WT (break)	1.62993	0.183
Manapal/WT (red)	1.08968	0.413