Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98983	0.83
27DAP/17DAP	1.11633	0.927
39DAP/27DAP	1.2682	1
41DAP/39DAP	1.78163	0.387
42DAP/41DAP	0.96471	1
43DAP/42DAP	0.99808	0.937
47DAP/43DAP	0.89981	0.645
52DAP/47DAP	1.33502	0.418
57DAP/52DAP	0.88296	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87093	0.044
17DAP/reference	1.02834	0.384
27DAP/reference	1.02102	0.623
39DAP/reference	0.98923	0.828
41DAP/reference	0.99151	0.814
42DAP/reference	0.94332	0.02
43DAP/reference	0.9976	0.904
47DAP/reference	0.99725	0.674
52DAP/reference	0.98424	0.546
57DAP/reference	0.93021	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92882	0.47
27DAP/17DAP	1.05678	0.909
39DAP/27DAP	1.07791	0.496
41DAP/39DAP	1.03596	1
42DAP/41DAP	1.00095	0.876
43DAP/42DAP	0.99566	0.991
47DAP/43DAP	1.02324	0.973
52DAP/47DAP	1.01169	1
57DAP/52DAP	0.98838	0.81
57DAP/7DAP	1.49122	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21483	0.325
17DAP/reference	1.46818	0.026
27DAP/reference	1.56658	0.008
39DAP/reference	1.70955	0.012
41DAP/reference	1.34886	0.117
42DAP/reference	1.41976	0.059
43DAP/reference	1.57255	0.013
47DAP/reference	1.15726	0.458
52DAP/reference	1.3768	0.013
57DAP/reference	1.31528	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9485	0.426
17DAP/reference	0.95229	0.253
27DAP/reference	0.859	0.097
39DAP/reference	0.95187	0.265
41DAP/reference	0.81439	0.01
42DAP/reference	0.83745	0.018
43DAP/reference	0.93902	0.43
47DAP/reference	0.89308	0.027
52DAP/reference	0.99808	0.761
57DAP/reference	0.94177	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56909	0.031
17DAP/reference	1.12908	0.578
27DAP/reference	1.43491	0.062
39DAP/reference	1.62225	0.019
41DAP/reference	1.3776	0.129
42DAP/reference	1.24214	0.204
43DAP/reference	0.94098	0.449
47DAP/reference	0.92598	0.174
52DAP/reference	1.41694	0.278
57DAP/reference	0.90808	0.247

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06187	0.966
26DAP/20DAP	0.81123	0.512
34DAP/26DAP	0.96415	0.92
51DAP/34DAP	1.00737	0.957
52DAP/51DAP	1.06253	0.689
53DAP/52DAP	1.07513	0.697
55DAP/53DAP	1.12422	0.452
57DAP/55DAP	1.03067	0.969
62DAP/57DAP	1.09278	0.935
68DAP/62DAP	1.04768	0.984
68DAP/14DAP	1.19182	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71087	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.4496	0.036
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.3769	0.224
Mature Eggplant/Ripe Tomato	0.35127	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92498	0.634
1-1-2/M82	0.90417	1
12-2/M82	1.20279
12-4/M82	0.98112	1
1-3/M82	0.97054	1
2-1-1/M82	1.16932	0.457
2-1/M82	N/A	N/A
2-6/M82	1.11816	0.505
3-2/M82	0.92048	1
4-1-1/M82	1.08062	1
4-1/M82	1.07377	0.853
4-3-2/M82	0.90419	1
4-3/M82	0.98951
5-3/M82	0.9579	1
6-2/M82	0.94739
6-3/M82	0.96938	1
7-1/M82	0.94797
7-2/M82	0.94826	0.313
9-3-2/M82	0.8633	1

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	0.89719
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.80955
IL1-4/WTpooled	0.83081	0.834
WT/WTpooled	N/A	N/A

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	1.62807	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05988	0.921
DC3000/delta hrp 6h	0.82861
DC3000/delta hrp 12h	1.12792	1
DC3000/delta hrp 24h	0.98728	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81477
DC3000 delta B/DC3000 delta AB	1.04825	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.61875	1
Exp 60h	1.24075	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.68728	1
Var 12h I row2-row1	1.22726	0.196
Var 12h NI row2-row1	0.88832	0.713
Var 36h I row2-row1	0.86849	0.805
Var 36h NI row2-row1	1.01499	1
Var 60h I row2-row1	1.28275	0.562
Var 60h NI row2-row1	1.24401	0.904
Time course 0hI-0hNI	1.12643	0.603
Time course 12hI-12hNI	0.95369	0.711
Time course 36hI-36hNI	1.04423	0.722
Time course 60hI-60hNI	2.79013	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)	1.36753	0.384
transgenic ySAMdc/azygous control (breaker)	0.77209	0.173
transgenic ySAMdc/azygous control (red)	1.27136	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0006	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9675	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.85948	0.183