Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9982	0.839
27DAP/17DAP	1.00818	1
39DAP/27DAP	0.92893	0.67
41DAP/39DAP	1.12288	1
42DAP/41DAP	0.82632	0.774
43DAP/42DAP	0.97315	0.895
47DAP/43DAP	0.8856	0.591
52DAP/47DAP	1.59006	0.372
57DAP/52DAP	0.86838	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05656	0.735
17DAP/reference	1.01919	0.843
27DAP/reference	0.89725	0.232
39DAP/reference	1.07611	0.27
41DAP/reference	1.1369	0.203
42DAP/reference	0.98881	0.455
43DAP/reference	1.05146	0.547
47DAP/reference	0.95521	0.345
52DAP/reference	0.9701	0.449
57DAP/reference	0.88433	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90545	0.35
27DAP/17DAP	1.04035	0.951
39DAP/27DAP	0.83056	0.215
41DAP/39DAP	1.09013	0.827
42DAP/41DAP	0.97942	0.777
43DAP/42DAP	0.96821	0.729
47DAP/43DAP	1.00083	1
52DAP/47DAP	1.002	0.93
57DAP/52DAP	0.85784	0.434
57DAP/7DAP	0.81604	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81282	0.095
17DAP/reference	0.80691	0.025
27DAP/reference	0.83388	0.01
39DAP/reference	0.78565	0.011
41DAP/reference	0.71465	0.022
42DAP/reference	0.57044	0.01
43DAP/reference	0.6807	0.022
47DAP/reference	0.79844	0.293
52DAP/reference	0.62702	0.024
57DAP/reference	0.63065	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1054	0.612
17DAP/reference	1.14416	0.415
27DAP/reference	1.0803	0.516
39DAP/reference	0.90428	0.136
41DAP/reference	0.88336	0.173
42DAP/reference	1.01184	1
43DAP/reference	1.39561	0.114
47DAP/reference	0.9771	0.349
52DAP/reference	0.99164	0.666
57DAP/reference	1.20277	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77511	0.029
17DAP/reference	1.06044	0.944
27DAP/reference	0.72675	0.026
39DAP/reference	0.76012	0.018
41DAP/reference	0.86816	0.025
42DAP/reference	0.80219	0.025
43DAP/reference	0.83373	0.057
47DAP/reference	0.99459	0.646
52DAP/reference	1.15553	0.979
57DAP/reference	0.93082	0.387

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95622	1
26DAP/20DAP	0.80272	0.512
34DAP/26DAP	1.44909	1
51DAP/34DAP	1.01429	0.909
52DAP/51DAP	1.23048	0.404
53DAP/52DAP	0.72353	0.055
55DAP/53DAP	1.00936	0.939
57DAP/55DAP	1.10918	0.841
62DAP/57DAP	1.344	1
68DAP/62DAP	0.88957	0.579
68DAP/14DAP	0.91548	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02241	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81776	0.336
Mature Green Tomato/Ripe Tomato	1.084	0.948
Immature Eggplant/Mature Eggplant	1.60471	0.051
Ripe Pepper/Ripe Tomato	1.05858	1
Mature Eggplant/Ripe Tomato	1.20077	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99545	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.02926	N/A
1-3/M82	0.71886	0.376
2-1-1/M82	1.28387	N/A
2-1/M82	N/A	N/A
2-6/M82	0.93421	N/A
3-2/M82	N/A	N/A
4-1-1/M82	1.23141	1
4-1/M82	0.95847	1
4-3-2/M82	0.80473	1
4-3/M82	N/A	N/A
5-3/M82	0.98215	1
6-2/M82	0.56529	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91476	N/A
9-3-2/M82	0.73577	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.44931	0.227
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.32542	0.792
IL7-3/WTpooled	1.38988	N/A
IL12-4/WTpooled	1.19331	0.839
IL1-4/WTpooled	0.81498	0.422
WT/WTpooled	1.10679	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	0.88613	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94558	0.941
DC3000/delta hrp 6h	1.26936	1
DC3000/delta hrp 12h	1.01627	1
DC3000/delta hrp 24h	1.19613	0.123

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	1.06697	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96224	1
Exp 36h	1.24519	1
Exp 60h	1.15195	0.205

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04448	1
Var 0h	0.73612	1
Var 12h I row2-row1	0.97318	0.77
Var 12h NI row2-row1	0.9382	0.494
Var 36h I row2-row1	0.81195	1
Var 36h NI row2-row1	1.00974	1
Var 60h I row2-row1	1.02406	1
Var 60h NI row2-row1	1.05851	0.904
Time course 0hI-0hNI	1.01996	0.867
Time course 12hI-12hNI	1.02683	0.818
Time course 36hI-36hNI	0.90431	0.198
Time course 60hI-60hNI	0.66084	0.007

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)	1.07419	0.397
transgenic ySAMdc/azygous control (breaker)	1.1303	0.248
transgenic ySAMdc/azygous control (red)	0.83718	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96794	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9475	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71683	1
Manapal/WT (break)	1.14857	0.14
Manapal/WT (red)	0.94826	0.728