Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.4.8.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05165	0.961
27DAP/17DAP	1.1163	0.849
39DAP/27DAP	0.82168	0.353
41DAP/39DAP	1.2239	0.67
42DAP/41DAP	1.0617	1
43DAP/42DAP	1.09802	1
47DAP/43DAP	1.07534	0.999
52DAP/47DAP	0.92084	0.746
57DAP/52DAP	1.07147	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84665	0.047
17DAP/reference	0.92402	0.111
27DAP/reference	1.06342	0.394
39DAP/reference	1.00589	0.828
41DAP/reference	1.03397	0.111
42DAP/reference	0.96044	0.233
43DAP/reference	0.91565	0.259
47DAP/reference	0.97096	0.392
52DAP/reference	0.82575	0.018
57DAP/reference	0.98863	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97869	0.629
27DAP/17DAP	1.00375	0.995
39DAP/27DAP	1.00935	0.799
41DAP/39DAP	1.00443	0.914
42DAP/41DAP	1.01865	0.886
43DAP/42DAP	1.03088	0.273
47DAP/43DAP	1.00322	0.973
52DAP/47DAP	0.97537	0.902
57DAP/52DAP	0.999	0.902
57DAP/7DAP	1.02595	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08818	0.338
17DAP/reference	0.94047	0.024
27DAP/reference	0.90935	0.014
39DAP/reference	0.98668	0.411
41DAP/reference	1.02599	0.614
42DAP/reference	0.99081	0.612
43DAP/reference	1.06278	0.289
47DAP/reference	1.07818	0.404
52DAP/reference	1.04567	0.401
57DAP/reference	1.08917	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00516	0.993
17DAP/reference	0.81653	0.043
27DAP/reference	0.88998	0.24
39DAP/reference	0.8531	0.113
41DAP/reference	1.01727	1
42DAP/reference	0.90771	0.169
43DAP/reference	1.14411	0.319
47DAP/reference	1.02362	0.89
52DAP/reference	1.01257	1
57DAP/reference	0.95027	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9406	0.29
17DAP/reference	0.98071	0.55
27DAP/reference	0.95701	0.147
39DAP/reference	1.02777	0.836
41DAP/reference	0.95027	0.096
42DAP/reference	0.99606	1
43DAP/reference	0.93465	0.226
47DAP/reference	1.01109	1
52DAP/reference	0.95097	0.518
57DAP/reference	1.02751	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01476	1
26DAP/20DAP	0.92362	0.512
34DAP/26DAP	1.01108	1
51DAP/34DAP	1.02122	0.829
52DAP/51DAP	1.00339	0.954
53DAP/52DAP	1.1056	0.58
55DAP/53DAP	0.9913	0.939
57DAP/55DAP	0.91531	0.76
62DAP/57DAP	1.08006	0.8
68DAP/62DAP	1.26933	0.142
68DAP/14DAP	1.26574	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01866	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.36201	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.42068	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97327	0.883
1-1-2/M82	0.97717	1
12-2/M82	0.97069	0.955
12-4/M82	1.07369	1
1-3/M82	0.75688	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.02103	0.695
3-2/M82	0.98601	1
4-1-1/M82	0.88744	1
4-1/M82	0.88904	1
4-3-2/M82	0.96576	1
4-3/M82	0.778	N/A
5-3/M82	1.10234	1
6-2/M82	1.05916	N/A
6-3/M82	1.09853	1
7-1/M82	1.00059	N/A
7-2/M82	0.94788	0.881
9-3-2/M82	0.89724	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0575	N/A
IL2-6/WTpooled	1.20213	0.419
IL7-5/WTpooled	0.60775	N/A
IL7-3/WTpooled	1.00639	1
IL12-4/WTpooled	0.7718	0.581
IL1-4/WTpooled	1.3243	N/A
WT/WTpooled	1.01823	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	0.9103	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82485	0.502
DC3000/delta hrp 6h	0.17441	N/A
DC3000/delta hrp 12h	1.15329	1
DC3000/delta hrp 24h	1.04635	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31654	0.11
DC3000 delta B/DC3000 delta AB	1.28839	0.112

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00932	1
Var 0h	0.67951	0.594
Var 12h I row2-row1	1.06781	0.692
Var 12h NI row2-row1	0.98628	1
Var 36h I row2-row1	0.80111	0.805
Var 36h NI row2-row1	1.00764	1
Var 60h I row2-row1	1.0182	1
Var 60h NI row2-row1	1.07352	0.904
Time course 0hI-0hNI	1.06133	0.764
Time course 12hI-12hNI	1.06916	0.654
Time course 36hI-36hNI	1.08789	0.147
Time course 60hI-60hNI	1.66535	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)	1.2346	0.541
transgenic ySAMdc/azygous control (breaker)	1.09748	0.172
transgenic ySAMdc/azygous control (red)	0.93408	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05649	0.041

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04273	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82333	1
Manapal/WT (break)	1.03367	1
Manapal/WT (red)	0.85669	0.274