Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.12.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98572	0.867
27DAP/17DAP	1.01056	1
39DAP/27DAP	1.03322	1
41DAP/39DAP	1.03288	0.814
42DAP/41DAP	1.12614	0.797
43DAP/42DAP	0.93364	0.598
47DAP/43DAP	0.96696	0.864
52DAP/47DAP	1.1117	0.798
57DAP/52DAP	1.02899	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13444	0.078
17DAP/reference	1.01071	0.606
27DAP/reference	0.99068	0.741
39DAP/reference	1.03816	0.256
41DAP/reference	0.99499	1
42DAP/reference	1.1365	0.011
43DAP/reference	1.00363	1
47DAP/reference	1.14048	0.048
52DAP/reference	1.15904	0.048
57DAP/reference	1.0609	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04539	0.525
27DAP/17DAP	0.98264	0.887
39DAP/27DAP	0.93709	0.54
41DAP/39DAP	1.30562	0.719
42DAP/41DAP	1.02746	0.947
43DAP/42DAP	1.04618	0.478
47DAP/43DAP	1.05005	0.699
52DAP/47DAP	0.90259	0.24
57DAP/52DAP	1.02847	0.838
57DAP/7DAP	1.02945	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02164	0.961
17DAP/reference	0.98508	0.295
27DAP/reference	0.98615	0.402
39DAP/reference	1.02254	0.297
41DAP/reference	1.02781	0.637
42DAP/reference	1.02161	0.686
43DAP/reference	0.98957	0.58
47DAP/reference	0.97957	0.504
52DAP/reference	0.94491	0.196
57DAP/reference	0.9844	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18237	0.12
17DAP/reference	1.26704	0.098
27DAP/reference	1.12336	0.345
39DAP/reference	1.06106	0.412
41DAP/reference	1.15675	0.241
42DAP/reference	1.14835	0.133
43DAP/reference	1.24655	0.176
47DAP/reference	1.00329	1
52DAP/reference	1.18011	0.026
57DAP/reference	1.16336	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02186	0.588
17DAP/reference	1.04468	0.456
27DAP/reference	0.97613	0.516
39DAP/reference	1.02097	0.496
41DAP/reference	0.99326	0.56
42DAP/reference	1.04401	0.481
43DAP/reference	1.11514	0.145
47DAP/reference	0.98021	0.525
52DAP/reference	1.05392	0.566
57DAP/reference	1.06528	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02778	0.966
26DAP/20DAP	1.04616	0.834
34DAP/26DAP	0.96413	0.94
51DAP/34DAP	1.04032	0.795
52DAP/51DAP	1.04598	0.626
53DAP/52DAP	1.11805	0.296
55DAP/53DAP	0.94905	0.5
57DAP/55DAP	0.98616	0.899
62DAP/57DAP	0.99275	1
68DAP/62DAP	0.90075	0.7
68DAP/14DAP	0.91761	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38629	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76456	0.223
Mature Green Tomato/Ripe Tomato	0.99445	0.715
Immature Eggplant/Mature Eggplant	0.82905	0.159
Ripe Pepper/Ripe Tomato	1.0922	1
Mature Eggplant/Ripe Tomato	0.48378	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1893	0.591
1-1-2/M82	1.05999	1
12-2/M82	1.04484	1
12-4/M82	0.94193	0.619
1-3/M82	0.89253
2-1-1/M82	0.98351
2-1/M82	N/A	N/A
2-6/M82	1.00291	1
3-2/M82	0.99144	1
4-1-1/M82	0.91204	1
4-1/M82	1.20133
4-3-2/M82	1.09603	1
4-3/M82	1.13825	1
5-3/M82	0.99288	1
6-2/M82	0.98183	1
6-3/M82	0.88815	1
7-1/M82	0.87963
7-2/M82	1.09035	0.324
9-3-2/M82	0.99632	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92064
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.89521
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.0411

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	1.13801	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96528	1
DC3000/delta hrp 6h	1.09887	1
DC3000/delta hrp 12h	1.01402	1
DC3000/delta hrp 24h	1.00393	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01061	1
DC3000 delta B/DC3000 delta AB	1.04606	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82924	1
Exp 36h	0.87962	0.749
Exp 60h	0.67866	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99707	1
Var 0h	1.14364	0.374
Var 12h I row2-row1	0.9864	1
Var 12h NI row2-row1	1.01167	1
Var 36h I row2-row1	1.13037	0.41
Var 36h NI row2-row1	0.97709	0.791
Var 60h I row2-row1	0.9115	0.832
Var 60h NI row2-row1	0.92261	0.756
Time course 0hI-0hNI	0.94861	0.59
Time course 12hI-12hNI	1.07053	0.313
Time course 36hI-36hNI	1.26111	0.007
Time course 60hI-60hNI	1.88777	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)	1.06927	0.287
transgenic ySAMdc/azygous control (breaker)	1.67421	0.172
transgenic ySAMdc/azygous control (red)	1.19122	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95174	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3776	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.41606	0.086
Manapal/WT (break)	1.85533	0.13
Manapal/WT (red)	2.44776	0.126