Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.3.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24356	0.133
27DAP/17DAP	1.60427	0.492
39DAP/27DAP	1.24239	0.426
41DAP/39DAP	0.87654	0.512
42DAP/41DAP	1.15025	0.876
43DAP/42DAP	1.24334	0.736
47DAP/43DAP	1.05491	0.965
52DAP/47DAP	1.02254	0.906
57DAP/52DAP	0.95657	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87897	0.048
17DAP/reference	0.9828	0.701
27DAP/reference	0.99983	0.904
39DAP/reference	0.95216	0.475
41DAP/reference	0.88484	0.114
42DAP/reference	0.8771	0.025
43DAP/reference	0.90763	0.211
47DAP/reference	0.92538	0.116
52DAP/reference	0.78175	0.026
57DAP/reference	0.98576	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99429	0.826
27DAP/17DAP	1.08908	0.887
39DAP/27DAP	1.35126	0.117
41DAP/39DAP	1.2148	0.19
42DAP/41DAP	0.92411	0.499
43DAP/42DAP	0.91888	0.189
47DAP/43DAP	1.00915	0.951
52DAP/47DAP	0.91992	0.719
57DAP/52DAP	0.89552	0.507
57DAP/7DAP	0.99651	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77306	0.072
17DAP/reference	0.90254	0.167
27DAP/reference	0.84923	0.071
39DAP/reference	0.77181	0.014
41DAP/reference	0.78703	0.056
42DAP/reference	0.66911	0.01
43DAP/reference	0.76154	0.033
47DAP/reference	0.82503	0.168
52DAP/reference	0.65676	0.028
57DAP/reference	0.80475	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8548	0.069
17DAP/reference	0.94957	0.109
27DAP/reference	0.96925	0.452
39DAP/reference	1.02849	0.912
41DAP/reference	0.87245	0.073
42DAP/reference	0.93507	0.067
43DAP/reference	0.94542	0.438
47DAP/reference	0.99121	0.59
52DAP/reference	0.8652	0.025
57DAP/reference	0.94733	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87056	0.077
17DAP/reference	0.85021	0.118
27DAP/reference	0.73019	0.03
39DAP/reference	0.85551	0.04
41DAP/reference	0.94451	0.371
42DAP/reference	0.93361	0.552
43DAP/reference	0.89671	0.206
47DAP/reference	0.83646	0.041
52DAP/reference	1.05135	0.952
57DAP/reference	0.85418	0.097

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9527	1
26DAP/20DAP	0.93654	0.512
34DAP/26DAP	1.10678	0.819
51DAP/34DAP	1.12299	0.759
52DAP/51DAP	1.12782	0.676
53DAP/52DAP	1.33254	0.149
55DAP/53DAP	1.12498	0.755
57DAP/55DAP	1.0816	0.935
62DAP/57DAP	1.02153	0.935
68DAP/62DAP	1.06062	0.926
68DAP/14DAP	0.77256	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.80065	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.51023	0.12
Mature Green Tomato/Ripe Tomato	0.96006	0.66
Immature Eggplant/Mature Eggplant	0.82402	0.111
Ripe Pepper/Ripe Tomato	0.51192	0.224
Mature Eggplant/Ripe Tomato	0.50566	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05263	0.742
1-1-2/M82	0.89395	N/A
12-2/M82	0.77863	0.74
12-4/M82	0.91046	0.33
1-3/M82	N/A	N/A
2-1-1/M82	1.40152	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.94714	N/A
4-1-1/M82	1.359	N/A
4-1/M82	0.80843	N/A
4-3-2/M82	0.90443	1
4-3/M82	0.72989	0.72
5-3/M82	1.3714	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.85516	1
7-2/M82	0.94781	0.796
9-3-2/M82	1.31327	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.34836	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.02113	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90981	0.868
DC3000/delta hrp 6h	0.79855	0.95
DC3000/delta hrp 12h	1.03269	1
DC3000/delta hrp 24h	1.0028	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02773	0.556
DC3000 delta B/DC3000 delta AB	0.9875	1

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	0.98856	1
Var 0h	0.93822	1
Var 12h I row2-row1	0.96857	0.948
Var 12h NI row2-row1	1.03935	1
Var 36h I row2-row1	1.14597	0.309
Var 36h NI row2-row1	1.30938	1
Var 60h I row2-row1	0.79282	0.374
Var 60h NI row2-row1	1.03676	1
Time course 0hI-0hNI	1.06811	0.833
Time course 12hI-12hNI	0.96388	0.719
Time course 36hI-36hNI	0.92053	0.28
Time course 60hI-60hNI	1.2452	0.037

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)	0.96899	0.789
transgenic ySAMdc/azygous control (breaker)	1.81791	0.172
transgenic ySAMdc/azygous control (red)	1.64362	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02473	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83815	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1792	0.096
Manapal/WT (break)	1.08705	1
Manapal/WT (red)	1.11622	1