Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.1.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88662	0.427
27DAP/17DAP	1.01188	0.913
39DAP/27DAP	1.41841	0.447
41DAP/39DAP	1.05136	0.859
42DAP/41DAP	1.24009	0.458
43DAP/42DAP	0.82863	0.708
47DAP/43DAP	0.94716	0.768
52DAP/47DAP	1.07444	0.987
57DAP/52DAP	1.08853	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92675	0.277
17DAP/reference	0.84142	0.069
27DAP/reference	0.95291	0.497
39DAP/reference	0.90787	0.234
41DAP/reference	0.75073	0.008
42DAP/reference	0.96907	0.268
43DAP/reference	1.06105	0.678
47DAP/reference	0.9788	0.445
52DAP/reference	1.08366	0.498
57DAP/reference	1.22289	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43847	0.184
27DAP/17DAP	0.91542	0.782
39DAP/27DAP	0.82541	0.127
41DAP/39DAP	1.85396	0.024
42DAP/41DAP	0.84509	0.14
43DAP/42DAP	0.71426	0.031
47DAP/43DAP	1.35815	0.133
52DAP/47DAP	1.27699	0.609
57DAP/52DAP	0.81185	0.352
57DAP/7DAP	0.95502	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93603	0.246
17DAP/reference	1.09436	0.328
27DAP/reference	1.21969	0.03
39DAP/reference	0.94629	0.23
41DAP/reference	0.94048	0.357
42DAP/reference	0.95159	0.355
43DAP/reference	0.95378	0.385
47DAP/reference	0.95612	0.504
52DAP/reference	0.94138	0.304
57DAP/reference	0.97928	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17784	0.463
17DAP/reference	0.72324	0.021
27DAP/reference	0.85076	0.084
39DAP/reference	1.5632	0.489
41DAP/reference	1.04522	0.862
42DAP/reference	1.02065	0.655
43DAP/reference	1.00508	0.706
47DAP/reference	1.0821	0.311
52DAP/reference	0.87371	0.131
57DAP/reference	0.83291	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0678	0.493
17DAP/reference	1.05353	0.638
27DAP/reference	1.21053	0.067
39DAP/reference	1.17366	0.025
41DAP/reference	1.19769	0.108
42DAP/reference	1.08821	0.47
43DAP/reference	1.08107	0.58
47DAP/reference	0.89412	0.174
52DAP/reference	1.03359	0.946
57DAP/reference	1.07608	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85263	0.733
26DAP/20DAP	0.81215	0.512
34DAP/26DAP	1.13461	1
51DAP/34DAP	0.70347	0.123
52DAP/51DAP	1.82753	N/A
53DAP/52DAP	1.12979	0.91
55DAP/53DAP	1.01237	1
57DAP/55DAP	0.64624	0.38
62DAP/57DAP	1.15798	N/A
68DAP/62DAP	1.19983	N/A
68DAP/14DAP	2.01204	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22331	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.29335	0.69
Immature Eggplant/Mature Eggplant	3.80292	N/A
Ripe Pepper/Ripe Tomato	0.40049	0.224
Mature Eggplant/Ripe Tomato	0.26179	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.98814	N/A
12-2/M82	1.13037	1
12-4/M82	0.98493	1
1-3/M82	N/A	N/A
2-1-1/M82	1.31449	1
2-1/M82	0.49197	N/A
2-6/M82	1.41053	N/A
3-2/M82	0.81777	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.33313	N/A
4-3-2/M82	N/A	N/A
4-3/M82	2.77412	0.268
5-3/M82	0.61505	0.447
6-2/M82	3.58004	0.219
6-3/M82	0.39242	N/A
7-1/M82	1.08092	1
7-2/M82	2.34475	N/A
9-3-2/M82	2.13845	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98837	1
IL2-6/WTpooled	1.12867	1
IL7-5/WTpooled	1.12214	0.792
IL7-3/WTpooled	0.90127	N/A
IL12-4/WTpooled	0.76274	0.581
IL1-4/WTpooled	0.82208	0.699
WT/WTpooled	0.97452	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	1.072	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96738	1
DC3000/delta hrp 6h	0.96134	0.95
DC3000/delta hrp 12h	0.91117	1
DC3000/delta hrp 24h	0.71496	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00054	N/A
DC3000 delta B/DC3000 delta AB	0.56745	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18004	1
Exp 36h	1.64899	0.489
Exp 60h	1.24042	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.91934	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.02774	1
transgenic ySAMdc/azygous control (breaker)	1.57075	0.248
transgenic ySAMdc/azygous control (red)	0.99534	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.19327	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62579	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.59112	0.083
Manapal/WT (break)	3.80436	0.13
Manapal/WT (red)	1.21127	0.863