Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89952	0.568
27DAP/17DAP	1.23143	0.849
39DAP/27DAP	0.96525	0.682
41DAP/39DAP	0.79774	0.343
42DAP/41DAP	1.03263	0.978
43DAP/42DAP	1.08013	0.993
47DAP/43DAP	0.71943	0.221
52DAP/47DAP	0.98792	0.924
57DAP/52DAP	1.09147	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13136	0.126
17DAP/reference	1.06175	0.239
27DAP/reference	0.98197	0.725
39DAP/reference	0.9348	0.221
41DAP/reference	0.93437	0.542
42DAP/reference	0.9575	0.278
43DAP/reference	0.81602
47DAP/reference	0.97115	0.366
52DAP/reference	0.8025	0.172
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63358	0.105
27DAP/17DAP	1.09583	0.915
39DAP/27DAP	0.98423	0.775
41DAP/39DAP	1.93174	0.012
42DAP/41DAP	0.7255	0.039
43DAP/42DAP	0.8762	0.224
47DAP/43DAP	1.65231	0.414
52DAP/47DAP	0.86457	0.777
57DAP/52DAP	1.09231	0.957
57DAP/7DAP	0.87517

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40607	0.141
17DAP/reference	1.22084	0.18
27DAP/reference	1.04467	0.974
39DAP/reference	1.13768	0.252
41DAP/reference	1.27444	0.043
42DAP/reference	1.26134	0.076
43DAP/reference	0.94489	0.334
47DAP/reference	0.97265	0.504
52DAP/reference	0.94725	0.332
57DAP/reference	1.08883	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10874	0.66
17DAP/reference	1.04938	0.658
27DAP/reference	0.99938	0.79
39DAP/reference	1.082	0.502
41DAP/reference	0.94998	0.348
42DAP/reference	0.89846	0.039
43DAP/reference	0.98233	0.681
47DAP/reference	0.88482	0.087
52DAP/reference	0.99996	0.761
57DAP/reference	0.94152	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52215	0.027
17DAP/reference	1.19376	0.518
27DAP/reference	1.15703	0.179
39DAP/reference	1.13806	0.034
41DAP/reference	1.14182	0.425
42DAP/reference	0.99587	0.816
43DAP/reference	1.02677	0.755
47DAP/reference	0.97079	0.465
52DAP/reference	1.26065	0.106
57DAP/reference	1.01398	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94882	1
26DAP/20DAP	0.94859	1
34DAP/26DAP	1.32214	0.819
51DAP/34DAP	0.73725	0.466
52DAP/51DAP	1.5232	0.503
53DAP/52DAP	0.83837	0.202
55DAP/53DAP	0.93708	0.709
57DAP/55DAP	1.24737	0.818
62DAP/57DAP	0.90183	0.466
68DAP/62DAP	0.86696	0.7
68DAP/14DAP	1.1103	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.72075	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98647	0.886
Mature Green Tomato/Ripe Tomato	0.72429	0.522
Immature Eggplant/Mature Eggplant	0.62386
Ripe Pepper/Ripe Tomato	0.80041	1
Mature Eggplant/Ripe Tomato	0.4758	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05355
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.18528	1
6-2/M82	2.43117	0.253
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.4895
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.50311	0.277
IL2-6/WTpooled	1.17706	0.659
IL7-5/WTpooled	1.60377	1
IL7-3/WTpooled	0.87424	1
IL12-4/WTpooled	1.19282	0.624
IL1-4/WTpooled	1.3515	1
WT/WTpooled	0.98437	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	1.39603	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95393	1
DC3000/delta hrp 6h	1.29293	0.978
DC3000/delta hrp 12h	1.0018	1
DC3000/delta hrp 24h	1.23207	0.051

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	0.24784

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90819	1
Exp 36h	1.00686	1
Exp 60h	1.04633	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02034
Var 0h	1.72348	0.259
Var 12h I row2-row1	0.75189
Var 12h NI row2-row1	1.01685	1
Var 36h I row2-row1	1.0284	1
Var 36h NI row2-row1	1.05163	1
Var 60h I row2-row1	0.77599
Var 60h NI row2-row1	1.1092	0.904
Time course 0hI-0hNI	1.04764	0.833
Time course 12hI-12hNI	1.06499	0.58
Time course 36hI-36hNI	1.39798	0.005
Time course 60hI-60hNI	1.74497	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)	1.12391	0.408
transgenic ySAMdc/azygous control (breaker)	0.74682	0.15
transgenic ySAMdc/azygous control (red)	0.99718	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97331	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08497	0.307
Manapal/WT (break)	1.00304	1
Manapal/WT (red)	0.66189	0.199