Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.4.17.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.5977	0.056
27DAP/17DAP	0.7823	0.422
39DAP/27DAP	1.45343	0.416
41DAP/39DAP	0.86469	0.558
42DAP/41DAP	1.69729	0.493
43DAP/42DAP	1.01161	0.937
47DAP/43DAP	1.09219	0.776
52DAP/47DAP	0.72771	0.378
57DAP/52DAP	1.25005	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78698	0.167
17DAP/reference	0.72017	0.007
27DAP/reference	0.85981	0.295
39DAP/reference	0.80614	0.083
41DAP/reference	0.70306	0.008
42DAP/reference	0.8108	0.001
43DAP/reference	0.88578	0.019
47DAP/reference	0.93168	0.127
52DAP/reference	1.0618	0.096
57DAP/reference	1.09398	0.22

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.90267	0.054
27DAP/17DAP	0.57813	0.1
39DAP/27DAP	1.34462	0.19
41DAP/39DAP	1.29616	0.043
42DAP/41DAP	0.90585	0.503
43DAP/42DAP	0.99709	0.774
47DAP/43DAP	1.12696	0.471
52DAP/47DAP	1.37948	0.209
57DAP/52DAP	1.43541	0.065
57DAP/7DAP	1.40212	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53153	0.043
17DAP/reference	1.49411	0.244
27DAP/reference	0.85748	0.135
39DAP/reference	1.40275	0.909
41DAP/reference	1.20751	0.723
42DAP/reference	1.10006	0.308
43DAP/reference	1.15098	0.788
47DAP/reference	1.37406	0.304
52DAP/reference	1.21331	0.212
57DAP/reference	1.09955	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8053	0.038
17DAP/reference	0.69738	0.007
27DAP/reference	0.80935	0.044
39DAP/reference	0.78702	0.017
41DAP/reference	0.91794	0.173
42DAP/reference	0.94536	0.289
43DAP/reference	0.89955	0.25
47DAP/reference	0.9339	0.097
52DAP/reference	0.96048	0.239
57DAP/reference	0.89071	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95535	0.071
17DAP/reference	1.24569	0.62
27DAP/reference	1.36104	0.049
39DAP/reference	1.32367	0.13
41DAP/reference	1.10018	0.818
42DAP/reference	0.80315	0.134
43DAP/reference	0.92507	0.432
47DAP/reference	0.94063	0.348
52DAP/reference	1.10381	0.609
57DAP/reference	1.09992	0.428

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90327	0.997
26DAP/20DAP	0.87268	1
34DAP/26DAP	0.73647	0.455
51DAP/34DAP	0.89895	0.624
52DAP/51DAP	1.63575	0.05
53DAP/52DAP	1.06075	0.901
55DAP/53DAP	1.05188	0.848
57DAP/55DAP	1.54383	0.274
62DAP/57DAP	0.46418	0.002
68DAP/62DAP	1.60725	0.029
68DAP/14DAP	1.15425	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47146	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96974	0.692
Mature Green Tomato/Ripe Tomato	0.85016	0.411
Immature Eggplant/Mature Eggplant	1.80983	0.05
Ripe Pepper/Ripe Tomato	2.03941	0.258
Mature Eggplant/Ripe Tomato	2.0086	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92293	0.944
1-1-2/M82	1.2047	0.977
12-2/M82	1.03399	1
12-4/M82	0.89486	1
1-3/M82	0.57551	0.378
2-1-1/M82	0.62278	0.465
2-1/M82	0.76088	N/A
2-6/M82	0.81412	N/A
3-2/M82	0.86187	N/A
4-1-1/M82	0.68603	0.908
4-1/M82	1.90801	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.09856	1
5-3/M82	1.19487	1
6-2/M82	1.08922	N/A
6-3/M82	1.11636	1
7-1/M82	0.68403	0.476
7-2/M82	0.87706	0.796
9-3-2/M82	1.60082	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02348	1
IL2-6/WTpooled	0.85964	0.473
IL7-5/WTpooled	1.00832	1
IL7-3/WTpooled	0.86582	0.418
IL12-4/WTpooled	0.90357	0.581
IL1-4/WTpooled	1.15183	1
WT/WTpooled	0.87087	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	0.84479	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90862	1
DC3000/delta hrp 6h	0.56309	0.489
DC3000/delta hrp 12h	1.02625	1
DC3000/delta hrp 24h	0.81805	0.092

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94295	0.629
DC3000 delta B/DC3000 delta AB	1.23901	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76933	1
Exp 36h	1.14914	1
Exp 60h	0.9153	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99552	1
Var 0h	0.99855	1
Var 12h I row2-row1	1.30854	0.406
Var 12h NI row2-row1	1.16044	0.649
Var 36h I row2-row1	1.1249	0.601
Var 36h NI row2-row1	1.62731	0.482
Var 60h I row2-row1	0.78878	0.287
Var 60h NI row2-row1	1.12958	0.904
Time course 0hI-0hNI	1.02664	1
Time course 12hI-12hNI	1.04111	0.833
Time course 36hI-36hNI	1.16423	0.355
Time course 60hI-60hNI	0.66381	0.047

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)	0.8828	0.246
transgenic ySAMdc/azygous control (breaker)	1.41252	0.248
transgenic ySAMdc/azygous control (red)	0.73075	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02045	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.67594	0.083
Manapal/WT (break)	0.57015	0.333
Manapal/WT (red)	0.68207	0.181