Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.2.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94623	0.683
27DAP/17DAP	0.96058	0.863
39DAP/27DAP	1.30891	0.416
41DAP/39DAP	0.99771	0.941
42DAP/41DAP	1.3049	0.792
43DAP/42DAP	1.21006	0.768
47DAP/43DAP	1.29129	0.609
52DAP/47DAP	1.16626	0.906
57DAP/52DAP	1.0304	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78929	0.118
17DAP/reference	0.80493	0.021
27DAP/reference	0.90617	0.304
39DAP/reference	0.86924	0.074
41DAP/reference	0.79047	0.018
42DAP/reference	0.92012	0.12
43DAP/reference	1.11013	0.05
47DAP/reference	1.07228	0.365
52DAP/reference	1.17175	0.229
57DAP/reference	1.21877	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13567	0.699
27DAP/17DAP	1.03644	0.9
39DAP/27DAP	0.87634	0.367
41DAP/39DAP	1.2501	0.455
42DAP/41DAP	1.04352	0.886
43DAP/42DAP	1.34181	0.045
47DAP/43DAP	0.9369	0.647
52DAP/47DAP	0.99765	0.962
57DAP/52DAP	1.12991	0.543
57DAP/7DAP	1.13882	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2968	0.11
17DAP/reference	1.1672	0.328
27DAP/reference	1.38656	0.006
39DAP/reference	1.36181	0.008
41DAP/reference	1.54336	0.033
42DAP/reference	1.52036	0.007
43DAP/reference	1.63587	0.007
47DAP/reference	1.27436	0.331
52DAP/reference	1.34878	0.048
57DAP/reference	1.40566	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82313	0.105
17DAP/reference	0.67093	0.005
27DAP/reference	0.94692	0.249
39DAP/reference	0.82234	0.076
41DAP/reference	0.99648	0.631
42DAP/reference	1.01802	1
43DAP/reference	0.69953	0.027
47DAP/reference	0.8847	0.026
52DAP/reference	0.86249	0.327
57DAP/reference	0.7106	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13424	0.575
17DAP/reference	1.06535	0.887
27DAP/reference	1.50296	0.027
39DAP/reference	1.28142	0.087
41DAP/reference	1.16755	0.047
42DAP/reference	1.38351	0.049
43DAP/reference	1.38534	0.059
47DAP/reference	0.98691	0.593
52DAP/reference	1.18883	0.155
57DAP/reference	1.57963	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03143	0.966
26DAP/20DAP	0.81951	0.512
34DAP/26DAP	0.67173	0.127
51DAP/34DAP	0.97149	0.824
52DAP/51DAP	0.67309	0.07
53DAP/52DAP	1.13142	0.895
55DAP/53DAP	0.8519	0.282
57DAP/55DAP	1.40539	0.682
62DAP/57DAP	1.0518	1
68DAP/62DAP	1.78881	0.139
68DAP/14DAP	2.95311	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44095	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63021	0.154
Mature Green Tomato/Ripe Tomato	0.5306	0.017
Immature Eggplant/Mature Eggplant	0.75494	0.134
Ripe Pepper/Ripe Tomato	1.3891	0.233
Mature Eggplant/Ripe Tomato	0.79858	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03607	1
1-1-2/M82	1.2507	1
12-2/M82	0.88767	0.955
12-4/M82	0.96853	1
1-3/M82	1.06374	1
2-1-1/M82	0.92216	0.92
2-1/M82	N/A	N/A
2-6/M82	1.20779	0.505
3-2/M82	0.94602	1
4-1-1/M82	1.13051	1
4-1/M82	0.77472
4-3-2/M82	1.48559	0.241
4-3/M82	1.34587	1
5-3/M82	1.08799	1
6-2/M82	1.09572	0.198
6-3/M82	0.98321	1
7-1/M82	0.99599	1
7-2/M82	1.30765	1
9-3-2/M82	1.24692	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80745	0.321
IL2-6/WTpooled	1.19388	0.584
IL7-5/WTpooled	1.67485	0.792
IL7-3/WTpooled	1.39033	1
IL12-4/WTpooled	1.08429	0.737
IL1-4/WTpooled	0.91685	0.834
WT/WTpooled	0.9697	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	0.80299	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96087	1
DC3000/delta hrp 6h	1.23865	0.582
DC3000/delta hrp 12h	0.9501	1
DC3000/delta hrp 24h	1.03054	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.8238	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.979	1
Exp 36h	1.01177	0.943
Exp 60h	0.90103	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9945	1
Var 0h	0.32382	1
Var 12h I row2-row1	0.88393	0.338
Var 12h NI row2-row1	1.11626	0.649
Var 36h I row2-row1	1.15137	1
Var 36h NI row2-row1	0.94093	0.225
Var 60h I row2-row1	0.94622	0.832
Var 60h NI row2-row1	0.83633	0.866
Time course 0hI-0hNI	0.88262	0.577
Time course 12hI-12hNI	0.96501	0.759
Time course 36hI-36hNI	0.99593	0.708
Time course 60hI-60hNI	0.63642	0.006

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)	1.02712	0.408
transgenic ySAMdc/azygous control (breaker)	0.96908	1
transgenic ySAMdc/azygous control (red)	0.99332	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03792	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01528	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40801	0.088
Manapal/WT (break)	1.46028	0.183
Manapal/WT (red)	0.92888	0.181