Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17327	0.477
27DAP/17DAP	1.23045	0.849
39DAP/27DAP	1.1724	0.915
41DAP/39DAP	0.76552	0.245
42DAP/41DAP	1.15531	0.92
43DAP/42DAP	0.9084	0.813
47DAP/43DAP	1.28675	0.633
52DAP/47DAP	0.76465	0.438
57DAP/52DAP	0.96315	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46728	0.008
17DAP/reference	0.55233	0.033
27DAP/reference	1.34111	0.771
39DAP/reference	0.57224	0.164
41DAP/reference	1.60545	0.014
42DAP/reference	1.11819	0.026
43DAP/reference	N/A	N/A
47DAP/reference	1.11091	0.114
52DAP/reference	0.46758	0.111
57DAP/reference	0.87743

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02528	1
27DAP/17DAP	1.08559	0.636
39DAP/27DAP	1.10331	0.499
41DAP/39DAP	0.8447	0.246
42DAP/41DAP	1.05942	0.879
43DAP/42DAP	1.00782	0.83
47DAP/43DAP	1.04438	0.563
52DAP/47DAP	0.9523	0.66
57DAP/52DAP	0.92344	0.225
57DAP/7DAP	1.04356	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94686	0.073
17DAP/reference	N/A	N/A
27DAP/reference	0.99631	0.571
39DAP/reference	1.00733	0.538
41DAP/reference	0.98455	0.311
42DAP/reference	1.03915	0.233
43DAP/reference	1.03578	0.289
47DAP/reference	0.9094	0.293
52DAP/reference	0.98896	0.679
57DAP/reference	0.95989	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03044	0.424
17DAP/reference	1.02677	0.557
27DAP/reference	0.84148	0.317
39DAP/reference	1.02875	0.783
41DAP/reference	0.82305	0.152
42DAP/reference	0.9005	0.02
43DAP/reference	1.16775	0.429
47DAP/reference	1.02588	0.994
52DAP/reference	1.01348	0.667
57DAP/reference	1.09676	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95889	0.526
17DAP/reference	0.97101	0.477
27DAP/reference	0.94848	0.376
39DAP/reference	1.02622	0.563
41DAP/reference	1.00277	1
42DAP/reference	1.00239	1
43DAP/reference	1.14744	0.541
47DAP/reference	0.95468	0.325
52DAP/reference	1.01531	0.904
57DAP/reference	0.86521	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00362	0.966
26DAP/20DAP	1.01313	1
34DAP/26DAP	1.16464	1
51DAP/34DAP	0.96267	0.743
52DAP/51DAP	1.06821	0.534
53DAP/52DAP	1.03475	0.868
55DAP/53DAP	0.97609	0.604
57DAP/55DAP	1.03055	1
62DAP/57DAP	0.91252	0.28
68DAP/62DAP	0.91019	0.747
68DAP/14DAP	1.02271	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02335	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84194	0.323
Mature Green Tomato/Ripe Tomato	1.27197	0.69
Immature Eggplant/Mature Eggplant	1.87371	0.05
Ripe Pepper/Ripe Tomato	0.73748	0.293
Mature Eggplant/Ripe Tomato	0.92462	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11795	0.536
1-1-2/M82	0.93917	0.958
12-2/M82	1.11777	1
12-4/M82	0.98761	1
1-3/M82	0.91127	0.501
2-1-1/M82	1.21318	0.689
2-1/M82	N/A	N/A
2-6/M82	0.99665	1
3-2/M82	N/A	N/A
4-1-1/M82	0.9147	0.668
4-1/M82	1.09284
4-3-2/M82	0.90888
4-3/M82	1.21738
5-3/M82	1.0103	1
6-2/M82	0.94299	0.497
6-3/M82	0.9805	1
7-1/M82	N/A	N/A
7-2/M82	0.97769	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80428	0.243
IL2-6/WTpooled	1.07827	0.788
IL7-5/WTpooled	0.66393	1
IL7-3/WTpooled	0.86897	0.418
IL12-4/WTpooled	1.00082	1
IL1-4/WTpooled	0.78175	0.562
WT/WTpooled	1.08079	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	1.20976	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9372	0.941
DC3000/delta hrp 6h	1.01446	1
DC3000/delta hrp 12h	0.98653	1
DC3000/delta hrp 24h	1.06209	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06769	0.476
DC3000 delta B/DC3000 delta AB	0.99224	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99308	1
Exp 36h	1.06334	1
Exp 60h	1.12659	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11139	1
Var 0h	0.87571	0.933
Var 12h I row2-row1	0.99725	1
Var 12h NI row2-row1	0.95458	0.82
Var 36h I row2-row1	0.98488	1
Var 36h NI row2-row1	0.80445	1
Var 60h I row2-row1	0.96212	0.439
Var 60h NI row2-row1	1.0125	1
Time course 0hI-0hNI	1.07809	0.297
Time course 12hI-12hNI	0.98034	0.769
Time course 36hI-36hNI	1.02155	0.881
Time course 60hI-60hNI	0.95444	0.319

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)	0.98036	0.485
transgenic ySAMdc/azygous control (breaker)	1.07308	1
transgenic ySAMdc/azygous control (red)	1.05397	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26077	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76961	1
Manapal/WT (break)	1.01095	1
Manapal/WT (red)	1.00071	0.863