Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.6.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85488	0.221
27DAP/17DAP	1.03505	0.92
39DAP/27DAP	0.8999	0.549
41DAP/39DAP	1.67476	0.225
42DAP/41DAP	1.31167	0.832
43DAP/42DAP	1.01622	0.945
47DAP/43DAP	1.11128	0.702
52DAP/47DAP	1.05628	0.982
57DAP/52DAP	0.87532	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97819	0.539
17DAP/reference	0.98492	0.701
27DAP/reference	0.94266	0.065
39DAP/reference	1.06366	0.016
41DAP/reference	1.07416	0.312
42DAP/reference	1.01762	0.523
43DAP/reference	1.0795	0.014
47DAP/reference	0.99952	0.764
52DAP/reference	1.02896	0.951
57DAP/reference	0.89763	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96385	0.484
27DAP/17DAP	0.98666	0.919
39DAP/27DAP	1.00368	1
41DAP/39DAP	1.02254	1
42DAP/41DAP	1.07256	0.773
43DAP/42DAP	1.00877	1
47DAP/43DAP	1.03115	0.963
52DAP/47DAP	0.94441	0.729
57DAP/52DAP	1.03643	0.874
57DAP/7DAP	1.2551	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83483	0.115
17DAP/reference	0.96718	0.389
27DAP/reference	0.9692	0.43
39DAP/reference	0.72867	0.014
41DAP/reference	0.86097	0.09
42DAP/reference	0.87968	0.136
43DAP/reference	0.76087	0.046
47DAP/reference	1.08774	0.685
52DAP/reference	0.77713	0.043
57DAP/reference	0.82871	0.048

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08188	0.269
17DAP/reference	1.09035	0.092
27DAP/reference	1.05512	0.704
39DAP/reference	1.08179	0.097
41DAP/reference	1.02512	1
42DAP/reference	1.03512	0.744
43DAP/reference	1.0282	0.892
47DAP/reference	1.02875	0.589
52DAP/reference	1.15051	0.007
57DAP/reference	1.10595	0.108

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81062	0.05
17DAP/reference	1.0357	0.728
27DAP/reference	0.81699	0.056
39DAP/reference	0.89539	0.101
41DAP/reference	0.88681	0.148
42DAP/reference	0.83258	0.134
43DAP/reference	0.96073	0.468
47DAP/reference	1.08375	0.279
52DAP/reference	0.88204	0.385
57DAP/reference	0.93188	0.288

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07192	0.966
26DAP/20DAP	0.85391	0.244
34DAP/26DAP	1.11699	0.819
51DAP/34DAP	0.87884	0.492
52DAP/51DAP	1.0097	1
53DAP/52DAP	1.01763	0.868
55DAP/53DAP	1.09277	0.325
57DAP/55DAP	1.09919	0.682
62DAP/57DAP	0.91505	0.994
68DAP/62DAP	0.72211	0.314
68DAP/14DAP	1.02983	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81118	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	383.039	0.417
Mature Green Tomato/Ripe Tomato	1.9514	0.016
Immature Eggplant/Mature Eggplant	0.81641	0.197
Ripe Pepper/Ripe Tomato	3.22825	1
Mature Eggplant/Ripe Tomato	1.19806	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00167
1-1-2/M82	1.15503
12-2/M82	N/A	N/A
12-4/M82	0.9193	1
1-3/M82	0.87243
2-1-1/M82	1.44
2-1/M82	N/A	N/A
2-6/M82	1.16581
3-2/M82	0.64001
4-1-1/M82	1.08801	1
4-1/M82	N/A	N/A
4-3-2/M82	1.07664
4-3/M82	N/A	N/A
5-3/M82	0.95356	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.04827
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02512	1
IL2-6/WTpooled	1.15724	0.46
IL7-5/WTpooled	0.67578
IL7-3/WTpooled	0.99222	1
IL12-4/WTpooled	0.88148	0.71
IL1-4/WTpooled	1.21411	1
WT/WTpooled	0.8621	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	1.12671	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12588	0.914
DC3000/delta hrp 6h	1.01736	1
DC3000/delta hrp 12h	1.05695	1
DC3000/delta hrp 24h	0.82901	0.088

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.6776	0.085
DC3000 delta B/DC3000 delta AB	0.83798	0.048

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94452	1
Exp 36h	0.83473	0.419
Exp 60h	0.77151	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.966	1
Var 0h	0.82584	1
Var 12h I row2-row1	0.94791	0.467
Var 12h NI row2-row1	0.95448	0.906
Var 36h I row2-row1	0.83135	0.438
Var 36h NI row2-row1	1.01019	1
Var 60h I row2-row1	1.23044	0.562
Var 60h NI row2-row1	1.18025	0.904
Time course 0hI-0hNI	1.05543	0.662
Time course 12hI-12hNI	1.01953	0.811
Time course 36hI-36hNI	0.88549	0.034
Time course 60hI-60hNI	0.83682	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)	0.92491	0.409
transgenic ySAMdc/azygous control (breaker)	1.12005	1
transgenic ySAMdc/azygous control (red)	1.01178	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00408	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.0303	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.48843	0.096
Manapal/WT (break)	0.89506	1
Manapal/WT (red)	1.88261	0.15