Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.13.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90354	0.232
27DAP/17DAP	1.12426	0.845
39DAP/27DAP	1.08054	0.919
41DAP/39DAP	0.89415	0.59
42DAP/41DAP	1.04503	0.933
43DAP/42DAP	0.97275	0.912
47DAP/43DAP	0.84321	0.504
52DAP/47DAP	0.98368	0.907
57DAP/52DAP	1.08692	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02595	0.872
17DAP/reference	0.9326	0.06
27DAP/reference	0.931	0.157
39DAP/reference	1.04373	0.734
41DAP/reference	1.02325	0.48
42DAP/reference	1.06113	0.01
43DAP/reference	1.03986	0.495
47DAP/reference	1.00836	1
52DAP/reference	0.9059	0.143
57DAP/reference	1.11018	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00969	1
27DAP/17DAP	1.0233	0.932
39DAP/27DAP	0.99646	1
41DAP/39DAP	0.92993	0.781
42DAP/41DAP	1.03124	0.861
43DAP/42DAP	1.03339	0.413
47DAP/43DAP	1.04611	0.756
52DAP/47DAP	0.96536	0.763
57DAP/52DAP	1.00379	1
57DAP/7DAP	0.95187	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04571	0.813
17DAP/reference	0.98864	0.518
27DAP/reference	0.9706	0.325
39DAP/reference	1.02968	0.411
41DAP/reference	1.03176	0.43
42DAP/reference	1.03782	0.534
43DAP/reference	1.03197	0.537
47DAP/reference	1.10083	0.259
52DAP/reference	1.09511	0.076
57DAP/reference	1.15859	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09257	0.284
17DAP/reference	0.9751	0.487
27DAP/reference	1.00678	0.79
39DAP/reference	1.05275	0.424
41DAP/reference	1.02861	0.737
42DAP/reference	0.99846	0.723
43DAP/reference	0.9265	0.175
47DAP/reference	1.08227	0.054
52DAP/reference	0.94028	0.078
57DAP/reference	0.98189	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0296	0.691
17DAP/reference	0.99925	0.855
27DAP/reference	0.98626	0.357
39DAP/reference	0.97518	0.299
41DAP/reference	0.97299	0.371
42DAP/reference	0.92984	0.049
43DAP/reference	0.94738	0.348
47DAP/reference	0.94974	0.139
52DAP/reference	0.95995	0.505
57DAP/reference	0.97318	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06348	0.43
26DAP/20DAP	1.12957	0.453
34DAP/26DAP	1.01705	1
51DAP/34DAP	1.02105	0.869
52DAP/51DAP	0.98514	1
53DAP/52DAP	1.0618	0.594
55DAP/53DAP	0.95904	0.686
57DAP/55DAP	0.98688
62DAP/57DAP	1.19403
68DAP/62DAP	1.01937	1
68DAP/14DAP	1.15205	0.045

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08093	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1093	0.089
Mature Green Tomato/Ripe Tomato	0.78293	0.411
Immature Eggplant/Mature Eggplant	1.43358	0.05
Ripe Pepper/Ripe Tomato	0.58687	1
Mature Eggplant/Ripe Tomato	0.3089	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00249	1
1-1-2/M82	0.99462	1
12-2/M82	0.95183	0.955
12-4/M82	1.00012	1
1-3/M82	0.94686	0.378
2-1-1/M82	0.88854	0.465
2-1/M82	1.2445	1
2-6/M82	0.96587	1
3-2/M82	1.04973	0.84
4-1-1/M82	0.99635	1
4-1/M82	0.99863	1
4-3-2/M82	0.85702	1
4-3/M82	0.91772	0.72
5-3/M82	0.97963	1
6-2/M82	0.98158	1
6-3/M82	1.02361	1
7-1/M82	1.02041	1
7-2/M82	0.94765	0.599
9-3-2/M82	0.83465	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88699	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.2605	0.362
IL12-4/WTpooled	1.06324	0.695
IL1-4/WTpooled	1.11579
WT/WTpooled	0.95706	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	1.9013	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98042	1
DC3000/delta hrp 6h	1.0726	0.95
DC3000/delta hrp 12h	0.92958	0.266
DC3000/delta hrp 24h	1.05116	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.40992	0.068
DC3000 delta B/DC3000 delta AB	1.25834	0.172

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.92455	0.943
Exp 60h	0.91796	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99696	1
Var 0h	1.10612	0.98
Var 12h I row2-row1	1.27998	0.242
Var 12h NI row2-row1	1.01587	1
Var 36h I row2-row1	1.17176	1
Var 36h NI row2-row1	1.02063	1
Var 60h I row2-row1	0.9898	0.832
Var 60h NI row2-row1	1.08167	0.904
Time course 0hI-0hNI	1.04886	0.867
Time course 12hI-12hNI	1.04199	0.773
Time course 36hI-36hNI	1.06353	0.114
Time course 60hI-60hNI	1.9315	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)	1.7904	0.261
transgenic ySAMdc/azygous control (breaker)	1.52168	1
transgenic ySAMdc/azygous control (red)	1.38935	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93896	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86973	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32771	0.307
Manapal/WT (break)	0.79066	1
Manapal/WT (red)	0.71271	0.216