Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07999	0.812
27DAP/17DAP	1.22877	0.92
39DAP/27DAP	1.48881	0.35
41DAP/39DAP	0.87641	0.566
42DAP/41DAP	1.46369	0.752
43DAP/42DAP	1.79044	0.682
47DAP/43DAP	1.10184	0.889
52DAP/47DAP	1.02095	0.781
57DAP/52DAP	1.45195	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00068	0.806
17DAP/reference	1.12152	0.047
27DAP/reference	1.01261	0.934
39DAP/reference	1.01942	0.771
41DAP/reference	1.0484	0.338
42DAP/reference	0.94493	0.163
43DAP/reference	1.021	0.838
47DAP/reference	0.98953	0.535
52DAP/reference	0.77579	0.027
57DAP/reference	0.82227	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00788	1
27DAP/17DAP	0.93742	0.58
39DAP/27DAP	1.06065	0.548
41DAP/39DAP	1.0355	0.876
42DAP/41DAP	0.96833	0.726
43DAP/42DAP	1.0236	0.513
47DAP/43DAP	0.9943	0.989
52DAP/47DAP	0.99594	0.962
57DAP/52DAP	1.023	0.963
57DAP/7DAP	1.09623	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87862	0.1
17DAP/reference	0.9191	0.021
27DAP/reference	0.8394	0.01
39DAP/reference	0.95261	0.064
41DAP/reference	0.904	0.018
42DAP/reference	0.89809	0.02
43DAP/reference	0.89011	0.012
47DAP/reference	0.87518	0.04
52DAP/reference	0.85205	0.022
57DAP/reference	0.88783	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08664	0.38
17DAP/reference	1.03407	0.806
27DAP/reference	0.87122	0.155
39DAP/reference	0.90479	0.095
41DAP/reference	0.84323	0.04
42DAP/reference	0.82889	0.017
43DAP/reference	1.00972	1
47DAP/reference	0.8804	0.021
52DAP/reference	0.97437	0.407
57DAP/reference	1.15752	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96189	0.068
17DAP/reference	0.96033	0.499
27DAP/reference	0.8731	0.03
39DAP/reference	0.88853	0.016
41DAP/reference	0.91255	0.055
42DAP/reference	0.7687	0.049
43DAP/reference	0.84398	0.095
47DAP/reference	0.96463	0.452
52DAP/reference	0.8243	0.082
57DAP/reference	0.54312	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06995	0.966
26DAP/20DAP	0.9274	0.512
34DAP/26DAP	1.01847	1
51DAP/34DAP	1.05154	0.613
52DAP/51DAP	0.99474	1
53DAP/52DAP	0.99038	0.938
55DAP/53DAP	0.94686	0.686
57DAP/55DAP	1.008	0.925
62DAP/57DAP	0.71782	0.05
68DAP/62DAP	0.89905	0.579
68DAP/14DAP	0.96202	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80766	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.10005	0.046
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.61007	0.092
Ripe Pepper/Ripe Tomato	5.61403	1
Mature Eggplant/Ripe Tomato	1.3293	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03892	1
1-1-2/M82	0.83906	N/A
12-2/M82	1.31673	1
12-4/M82	0.98561	1
1-3/M82	0.81868	0.378
2-1-1/M82	1.24201	0.764
2-1/M82	1.27861	1
2-6/M82	1.27902	0.505
3-2/M82	0.76924	N/A
4-1-1/M82	1.26611	0.782
4-1/M82	1.09598	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.88426	1
5-3/M82	0.95438	1
6-2/M82	0.94036	1
6-3/M82	1.06275	1
7-1/M82	N/A	N/A
7-2/M82	1.23836	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82353	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.79584	1
IL7-3/WTpooled	0.83187	N/A
IL12-4/WTpooled	1.35158	0.525
IL1-4/WTpooled	1.02153	1
WT/WTpooled	1.15303	0.686

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	0.97158	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95815	1
DC3000/delta hrp 6h	1.01518	1
DC3000/delta hrp 12h	1.2175	1
DC3000/delta hrp 24h	1.04451	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03371	0.648
DC3000 delta B/DC3000 delta AB	1.0133	0.738

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9902	1
Exp 36h	0.77342	0.456
Exp 60h	1.03759	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99802	1
Var 0h	0.52125	1
Var 12h I row2-row1	1.09512	0.272
Var 12h NI row2-row1	0.91751	0.546
Var 36h I row2-row1	1.16075	1
Var 36h NI row2-row1	0.94017	0.522
Var 60h I row2-row1	1.2335	0.562
Var 60h NI row2-row1	1.19675	0.904
Time course 0hI-0hNI	1.14732	0.63
Time course 12hI-12hNI	1.00719	0.9
Time course 36hI-36hNI	1.05728	0.355
Time course 60hI-60hNI	1.15983	0.042

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)	1.07506	0.283
transgenic ySAMdc/azygous control (breaker)	0.89123	0.49
transgenic ySAMdc/azygous control (red)	0.98547	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10524	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99284	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68637	0.172
Manapal/WT (break)	0.85001	1
Manapal/WT (red)	1.11992	1