Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.1.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06131	1
27DAP/17DAP	0.92642	0.873
39DAP/27DAP	0.81191	0.512
41DAP/39DAP	1.83259	0.286
42DAP/41DAP	0.95664	1
43DAP/42DAP	0.87539	0.77
47DAP/43DAP	0.94923	0.76
52DAP/47DAP	1.69914	0.26
57DAP/52DAP	0.86519	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.994	0.727
17DAP/reference	0.96798	0.474
27DAP/reference	1.01333	0.981
39DAP/reference	1.01304	0.903
41DAP/reference	0.98998	0.667
42DAP/reference	0.96489	0.12
43DAP/reference	1.15974	0.014
47DAP/reference	0.92416	0.046
52DAP/reference	0.95477	0.427
57DAP/reference	1.22727	0.033

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82058	0.201
27DAP/17DAP	1.0508	0.924
39DAP/27DAP	1.13597	0.441
41DAP/39DAP	0.97687	0.98
42DAP/41DAP	1.0782	0.872
43DAP/42DAP	1.11379	0.513
47DAP/43DAP	1.01126	1
52DAP/47DAP	0.90856	0.624
57DAP/52DAP	0.86267	0.428
57DAP/7DAP	1.06318	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07832	0.6
17DAP/reference	0.88293	0.031
27DAP/reference	0.83946	0.01
39DAP/reference	0.82208	0.011
41DAP/reference	0.86376	0.038
42DAP/reference	0.87892	0.01
43DAP/reference	0.80294	0.015
47DAP/reference	0.92671	0.383
52DAP/reference	0.82973	0.017
57DAP/reference	0.7934	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95467	0.399
17DAP/reference	0.95204	0.326
27DAP/reference	1.12858	0.254
39DAP/reference	1.06471	0.848
41DAP/reference	1.018	1
42DAP/reference	0.96434	0.355
43DAP/reference	1.01254	0.863
47DAP/reference	0.97425	0.434
52DAP/reference	0.89735	0.014
57DAP/reference	0.88888	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83742	0.03
17DAP/reference	0.99998	0.886
27DAP/reference	0.82158	0.089
39DAP/reference	0.88954	0.076
41DAP/reference	0.84834	0.03
42DAP/reference	0.87891	0.059
43DAP/reference	0.94785	0.398
47DAP/reference	0.97668	0.478
52DAP/reference	0.77286	0.141
57DAP/reference	1.13931	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9271	0.89
26DAP/20DAP	0.86995	0.244
34DAP/26DAP	1.25034	0.819
51DAP/34DAP	1.66237	0.044
52DAP/51DAP	0.9236	0.151
53DAP/52DAP	4.29626	0.018
55DAP/53DAP	1.3939	0.042
57DAP/55DAP	1.00329	0.855
62DAP/57DAP	0.23722	0.002
68DAP/62DAP	1.97916	0.533
68DAP/14DAP	1.04167	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80253	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18485	0.058
Mature Green Tomato/Ripe Tomato	0.80028	0.287
Immature Eggplant/Mature Eggplant	0.83214	0.105
Ripe Pepper/Ripe Tomato	1.01036	1
Mature Eggplant/Ripe Tomato	0.99104	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07973	1
1-1-2/M82	0.87692	0.958
12-2/M82	1.16358	0.389
12-4/M82	0.94332	1
1-3/M82	0.92296	0.501
2-1-1/M82	1.15169	0.689
2-1/M82	N/A	N/A
2-6/M82	1.04534	0.594
3-2/M82	0.86987	1
4-1-1/M82	1.07606	1
4-1/M82	0.84776	1
4-3-2/M82	0.92235	1
4-3/M82	0.88956	1
5-3/M82	0.98122	1
6-2/M82	0.95738	1
6-3/M82	1.2708
7-1/M82	1.00249	1
7-2/M82	1.06531	1
9-3-2/M82	0.90973	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94936	1
IL2-6/WTpooled	1.38697
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.27137
IL12-4/WTpooled	0.34641
IL1-4/WTpooled	1.35405	0.426
WT/WTpooled	1.35132	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	0.82935	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02983	0.921
DC3000/delta hrp 6h	0.83429	0.95
DC3000/delta hrp 12h	0.97408	1
DC3000/delta hrp 24h	1.06621	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73468
DC3000 delta B/DC3000 delta AB	1.00549	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92264	1
Exp 36h	1.0909	1
Exp 60h	0.9415	0.855

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	1.17663	0.311
Var 12h I row2-row1	1.03055
Var 12h NI row2-row1	1.45878
Var 36h I row2-row1	0.89267
Var 36h NI row2-row1	1.21681
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.58087	0.904
Time course 0hI-0hNI	0.97556	0.979
Time course 12hI-12hNI	1.00496	1
Time course 36hI-36hNI	0.9655	0.589
Time course 60hI-60hNI	1.04477	0.673

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)	1.01779	0.571
transgenic ySAMdc/azygous control (breaker)	1.12959	0.248
transgenic ySAMdc/azygous control (red)	1.0178	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14898	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97929	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76078	1
Manapal/WT (break)	0.84203	0.333
Manapal/WT (red)	1.18522	0.413