Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94918	0.61
27DAP/17DAP	1.00707	0.947
39DAP/27DAP	1.70075	0.13
41DAP/39DAP	1.19571	0.403
42DAP/41DAP	1.25198	0.73
43DAP/42DAP	0.97084	0.912
47DAP/43DAP	0.87129	0.55
52DAP/47DAP	1.18651	0.626
57DAP/52DAP	1.27595	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00531	1
17DAP/reference	1.08128	0.096
27DAP/reference	1.0025	1
39DAP/reference	0.99323	0.901
41DAP/reference	1.06342	0.552
42DAP/reference	0.92352	0.041
43DAP/reference	1.0603	0.495
47DAP/reference	0.94337	0.207
52DAP/reference	0.86037	0.158
57DAP/reference	0.82588	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22984	0.319
27DAP/17DAP	1.10832	0.905
39DAP/27DAP	1.07083	0.758
41DAP/39DAP	1.33105	1
42DAP/41DAP	1.21665	0.539
43DAP/42DAP	0.85588	0.224
47DAP/43DAP	1.04107	0.969
52DAP/47DAP	1.15233	0.645
57DAP/52DAP	1.37728	0.199
57DAP/7DAP	0.9328

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21936	0.059
17DAP/reference	1.14898	0.147
27DAP/reference	1.07587	0.088
39DAP/reference	1.4207	0.006
41DAP/reference	1.44356	0.021
42DAP/reference	1.42762	0.008
43DAP/reference	1.45845	0.007
47DAP/reference	1.43218	0.106
52DAP/reference	1.50675	0.009
57DAP/reference	1.42771	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09419	0.226
17DAP/reference	1.03487	0.584
27DAP/reference	0.99491	0.735
39DAP/reference	0.98799	0.569
41DAP/reference	0.91195	0.268
42DAP/reference	1.03166	0.899
43DAP/reference	1.03667	0.892
47DAP/reference	1.17059	0.218
52DAP/reference	1.00888	1
57DAP/reference	1.15964	0.033

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15788	0.338
17DAP/reference	1.04883	0.784
27DAP/reference	1.06785	0.934
39DAP/reference	1.2497	0.097
41DAP/reference	1.04102	0.734
42DAP/reference	1.02174	1
43DAP/reference	1.26891	0.139
47DAP/reference	0.94659	0.371
52DAP/reference	1.11692	0.649
57DAP/reference	1.40064	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03384	1
26DAP/20DAP	1.9195	0.166
34DAP/26DAP	1.06365	1
51DAP/34DAP	2.32982	0.035
52DAP/51DAP	0.89842	1
53DAP/52DAP	1.6611	0.643
55DAP/53DAP	0.77858	0.544
57DAP/55DAP	0.83455	0.527
62DAP/57DAP	1.13037
68DAP/62DAP	1.96336
68DAP/14DAP	0.69858

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11452	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29255	0.089
Mature Green Tomato/Ripe Tomato	0.93073	0.66
Immature Eggplant/Mature Eggplant	1.11155	0.439
Ripe Pepper/Ripe Tomato	0.96348
Mature Eggplant/Ripe Tomato	0.81489

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.7181
1-1-2/M82	0.6548
12-2/M82	N/A	N/A
12-4/M82	0.99735	1
1-3/M82	0.65453
2-1-1/M82	1.72217
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.83362
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.80309
4-3/M82	1.05176	1
5-3/M82	0.92085	0.364
6-2/M82	N/A	N/A
6-3/M82	1.15728
7-1/M82	N/A	N/A
7-2/M82	0.78192
9-3-2/M82	1.10846

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.42028	0.243
IL2-6/WTpooled	1.14271	0.659
IL7-5/WTpooled	1.09893	0.792
IL7-3/WTpooled	0.47007	0.294
IL12-4/WTpooled	0.79269	0.581
IL1-4/WTpooled	0.81934	0.457
WT/WTpooled	1.07617	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	1.13071	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08955	0.921
DC3000/delta hrp 6h	0.94223	0.95
DC3000/delta hrp 12h	1.09253	1
DC3000/delta hrp 24h	1.7389	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19593	0.042
DC3000 delta B/DC3000 delta AB	1.39817	0.095

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01565	1
Exp 36h	1.26038	1
Exp 60h	1.34279	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03097	1
Var 0h	1.33316	0.325
Var 12h I row2-row1	1.4846	0.506
Var 12h NI row2-row1	1.1958	0.649
Var 36h I row2-row1	1.0261	1
Var 36h NI row2-row1	1.02106	1
Var 60h I row2-row1	0.69012	0.285
Var 60h NI row2-row1	1.05297	1
Time course 0hI-0hNI	0.978	0.917
Time course 12hI-12hNI	1.16035	0.493
Time course 36hI-36hNI	1.18408	0.19
Time course 60hI-60hNI	1.86459	0.009

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)	0.89661	0.377
transgenic ySAMdc/azygous control (breaker)	0.63992	0.15
transgenic ySAMdc/azygous control (red)	0.89709	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01569	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99018	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84947	0.172
Manapal/WT (break)	1.24529	0.14
Manapal/WT (red)	0.72066	0.181