Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.6.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13294	0.681
27DAP/17DAP	1.0374	1
39DAP/27DAP	0.75368	0.27
41DAP/39DAP	1.04423	0.88
42DAP/41DAP	1.03087	1
43DAP/42DAP	1.0847	0.991
47DAP/43DAP	1.26758	0.442
52DAP/47DAP	1.10414	0.902
57DAP/52DAP	1.16182	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96766	0.503
17DAP/reference	1.03603	0.508
27DAP/reference	1.01978	0.863
39DAP/reference	1.05094	0.76
41DAP/reference	0.90966	0.267
42DAP/reference	1.01975	1
43DAP/reference	1.12297	0.133
47DAP/reference	1.04113	0.91
52DAP/reference	1.28677	0.038
57DAP/reference	1.11484	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04158	0.934
27DAP/17DAP	0.79264	0.724
39DAP/27DAP	0.92995	0.616
41DAP/39DAP	1.09062	0.817
42DAP/41DAP	0.90688	0.425
43DAP/42DAP	1.10178	0.478
47DAP/43DAP	1.17111	0.674
52DAP/47DAP	0.87984	0.6
57DAP/52DAP	0.97723	0.756
57DAP/7DAP	0.92807	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06498	0.91
17DAP/reference	1.09379	0.754
27DAP/reference	0.94207	0.402
39DAP/reference	1.06564	1
41DAP/reference	1.09983	0.56
42DAP/reference	1.04162	0.713
43DAP/reference	0.98235	0.555
47DAP/reference	1.26094	0.285
52DAP/reference	1.06619	0.401
57DAP/reference	1.15891	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25133	0.531
17DAP/reference	1.0729	0.375
27DAP/reference	0.9968	0.663
39DAP/reference	1.11874	0.272
41DAP/reference	0.95665	0.459
42DAP/reference	0.92548	0.261
43DAP/reference	0.91797	0.394
47DAP/reference	0.88689	0.047
52DAP/reference	1.19398
57DAP/reference	1.06343	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18561	0.709
17DAP/reference	0.86839	0.488
27DAP/reference	1.18734
39DAP/reference	1.0312	0.885
41DAP/reference	1.21779	0.265
42DAP/reference	1.03429	0.893
43DAP/reference	1.17449	0.499
47DAP/reference	0.93282	0.315
52DAP/reference	1.45069	0.123
57DAP/reference	1.03222	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95363	1
26DAP/20DAP	0.91197	1
34DAP/26DAP	0.96275	0.944
51DAP/34DAP	1.30052	0.869
52DAP/51DAP	1.206	0.377
53DAP/52DAP	1.00873	0.902
55DAP/53DAP	1.18783	0.387
57DAP/55DAP	1.09932	0.94
62DAP/57DAP	0.66482	0.028
68DAP/62DAP	1.67917	0.007
68DAP/14DAP	1.71219	0.125

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89092	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23955	0.058
Mature Green Tomato/Ripe Tomato	0.85176	0.522
Immature Eggplant/Mature Eggplant	0.96147	0.808
Ripe Pepper/Ripe Tomato	1.3385	0.256
Mature Eggplant/Ripe Tomato	0.80196	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88249
1-1-2/M82	0.92281	1
12-2/M82	N/A	N/A
12-4/M82	0.81754
1-3/M82	N/A	N/A
2-1-1/M82	0.65259
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.19086
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.03261	1
6-2/M82	N/A	N/A
6-3/M82	1.02611
7-1/M82	1.08503
7-2/M82	1.0376
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78459	0.321
IL2-6/WTpooled	1.44292	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9698	1
IL12-4/WTpooled	1.1876	0.367
IL1-4/WTpooled	0.90167	0.562
WT/WTpooled	0.98041	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	0.8725	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05781	0.921
DC3000/delta hrp 6h	1.06802	1
DC3000/delta hrp 12h	0.91038	1
DC3000/delta hrp 24h	1.02973	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.52039

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02861	1
Exp 36h	1.67225	0.693
Exp 60h	1.51722	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89295	1
Var 0h	1.05776	0.98
Var 12h I row2-row1	1.03284	1
Var 12h NI row2-row1	0.6896	0.713
Var 36h I row2-row1	0.67145	1
Var 36h NI row2-row1	1.02284	1
Var 60h I row2-row1	1.09686	0.483
Var 60h NI row2-row1	0.73745	1
Time course 0hI-0hNI	0.82719	1
Time course 12hI-12hNI	1.05279	0.72
Time course 36hI-36hNI	0.95191	0.389
Time course 60hI-60hNI	0.84213	0.015

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)	1.13947	0.325
transgenic ySAMdc/azygous control (breaker)	1.07422	1
transgenic ySAMdc/azygous control (red)	0.99246	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95288	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85427	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90339	1
Manapal/WT (break)	1.13522	0.381
Manapal/WT (red)	1.10646	1