Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.12.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43288	0.394
27DAP/17DAP	1.1231	0.883
39DAP/27DAP	1.29713	0.516
41DAP/39DAP	0.8239	0.385
42DAP/41DAP	1.06918	1
43DAP/42DAP	0.95824	0.709
47DAP/43DAP	1.20865	0.68
52DAP/47DAP	0.93728	0.771
57DAP/52DAP	1.06302	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19231	0.057
17DAP/reference	1.21686	0.148
27DAP/reference	1.12256	0.375
39DAP/reference	0.98501	0.75
41DAP/reference	1.25695	0.145
42DAP/reference	1.29351	0.002
43DAP/reference	1.19922	0.152
47DAP/reference	1.29307	0.004
52DAP/reference	1.27156	0.023
57DAP/reference	1.29949	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92286	0.442
27DAP/17DAP	0.96005	0.684
39DAP/27DAP	1.05045	0.646
41DAP/39DAP	1.05409	0.65
42DAP/41DAP	0.97052	0.708
43DAP/42DAP	1.07072	0.273
47DAP/43DAP	0.99271	0.971
52DAP/47DAP	1.03653	0.856
57DAP/52DAP	1.00728	1
57DAP/7DAP	1.05651	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11137	0.524
17DAP/reference	0.99481	0.693
27DAP/reference	0.99566	0.614
39DAP/reference	0.82693	0.049
41DAP/reference	0.9299	0.357
42DAP/reference	0.78705	0.016
43DAP/reference	0.76789	0.059
47DAP/reference	0.97925	0.671
52DAP/reference	0.90888	0.066
57DAP/reference	1.18531	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30255	0.07
17DAP/reference	1.38133	0.016
27DAP/reference	1.22984	0.041
39DAP/reference	1.33675	0.207
41DAP/reference	1.37506	0.034
42DAP/reference	1.2904	0.028
43DAP/reference	1.22331	0.055
47DAP/reference	1.22099	0.017
52DAP/reference	1.0831	0.667
57DAP/reference	1.84953	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03105	0.75
17DAP/reference	1.08411	0.699
27DAP/reference	1.04762	0.298
39DAP/reference	0.98979	0.643
41DAP/reference	0.91067	0.237
42DAP/reference	0.95382	0.552
43DAP/reference	0.99134	0.639
47DAP/reference	1.13203	0.187
52DAP/reference	0.80091	0.184
57DAP/reference	1.20699	0.347

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.6231	0.328
26DAP/20DAP	1.06688	0.689
34DAP/26DAP	1.1079	0.542
51DAP/34DAP	1.0303	0.909
52DAP/51DAP	1.04995	0.651
53DAP/52DAP	0.90755	0.336
55DAP/53DAP	1.05818	0.842
57DAP/55DAP	1.06709	0.793
62DAP/57DAP	1.07769	0.868
68DAP/62DAP	1.03206	0.939
68DAP/14DAP	0.57513	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02897	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.19878	0.058
Mature Green Tomato/Ripe Tomato	1.06282	0.774
Immature Eggplant/Mature Eggplant	0.23508	N/A
Ripe Pepper/Ripe Tomato	1.77756	1
Mature Eggplant/Ripe Tomato	0.69514	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.18937	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.40171	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.84961	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97004	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85828	0.418
IL12-4/WTpooled	0.96001	1
IL1-4/WTpooled	0.99517	1
WT/WTpooled	0.95211	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	0.91207	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99821	1
DC3000/delta hrp 6h	1.02553	0.95
DC3000/delta hrp 12h	0.7421	N/A
DC3000/delta hrp 24h	1.02116	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91527	0.196
DC3000 delta B/DC3000 delta AB	0.97691	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97425	1
Exp 36h	N/A	N/A
Exp 60h	1.12322	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98092	1
Var 0h	1.13196	1
Var 12h I row2-row1	0.93542	0.565
Var 12h NI row2-row1	1.1045	0.649
Var 36h I row2-row1	0.89429	1
Var 36h NI row2-row1	1.12682	0.276
Var 60h I row2-row1	1.027	1
Var 60h NI row2-row1	1.07539	0.904
Time course 0hI-0hNI	0.95716	0.675
Time course 12hI-12hNI	1.007	0.885
Time course 36hI-36hNI	0.95657	0.302
Time course 60hI-60hNI	0.72712	0.008

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)	0.97037	0.614
transgenic ySAMdc/azygous control (breaker)	1.3218	0.165
transgenic ySAMdc/azygous control (red)	0.97466	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01836	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00546	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.76252	0.083
Manapal/WT (break)	1.39801	0.14
Manapal/WT (red)	1.19435	0.222