Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85416	0.339
27DAP/17DAP	1.25097	0.825
39DAP/27DAP	1.05931	0.946
41DAP/39DAP	0.88983	0.561
42DAP/41DAP	0.91489	1
43DAP/42DAP	0.95287	0.9
47DAP/43DAP	1.08325	0.776
52DAP/47DAP	1.23826	0.791
57DAP/52DAP	1.04055	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98411	0.601
17DAP/reference	0.99165	0.819
27DAP/reference	1.06737	0.375
39DAP/reference	1.01054	0.871
41DAP/reference	0.98209	0.667
42DAP/reference	0.86836	0.003
43DAP/reference	0.94845	0.259
47DAP/reference	0.89429	0.01
52DAP/reference	1.01164	0.689
57DAP/reference	0.91585	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7044	0.045
27DAP/17DAP	1.21917	0.25
39DAP/27DAP	0.88457	0.316
41DAP/39DAP	1.03235	0.88
42DAP/41DAP	1.0481	0.773
43DAP/42DAP	0.70722	0.022
47DAP/43DAP	1.10487	0.234
52DAP/47DAP	0.90768	0.316
57DAP/52DAP	0.96274	0.68
57DAP/7DAP	0.79106	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03768	1
17DAP/reference	0.99733	0.693
27DAP/reference	0.86972	0.055
39DAP/reference	0.93178	0.083
41DAP/reference	0.971	0.412
42DAP/reference	1.02239	1
43DAP/reference	1.03099	0.746
47DAP/reference	0.97803	0.671
52DAP/reference	0.88443	0.083
57DAP/reference	1.04942	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03964	0.802
17DAP/reference	0.8938	0.063
27DAP/reference	0.92917	0.292
39DAP/reference	0.79675	0.013
41DAP/reference	0.78195	0.028
42DAP/reference	0.83155	0.019
43DAP/reference	0.91005	0.257
47DAP/reference	0.9165	0.094
52DAP/reference	0.78252	0.004
57DAP/reference	0.86864	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91108	0.422
17DAP/reference	0.92426	0.281
27DAP/reference	0.97605	0.624
39DAP/reference	0.91493	0.101
41DAP/reference	0.94345	0.459
42DAP/reference	0.81488	0.071
43DAP/reference	0.76587	0.038
47DAP/reference	0.91267	0.097
52DAP/reference	0.8707	0.247
57DAP/reference	0.87556	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02479	1
26DAP/20DAP	0.78502	0.228
34DAP/26DAP	0.74839	0.186
51DAP/34DAP	0.88286	0.209
52DAP/51DAP	1.04063	0.651
53DAP/52DAP	1.1931	0.334
55DAP/53DAP	1.08974	0.893
57DAP/55DAP	1.07581	0.969
62DAP/57DAP	0.96157	0.871
68DAP/62DAP	1.02617	0.939
68DAP/14DAP	0.98661	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82459	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95166	0.648
Mature Green Tomato/Ripe Tomato	1.10488	0.437
Immature Eggplant/Mature Eggplant	1.53565	0.05
Ripe Pepper/Ripe Tomato	2.28893	1
Mature Eggplant/Ripe Tomato	4.18015	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07509	1
1-1-2/M82	0.87377	1
12-2/M82	1.14153	0.448
12-4/M82	0.80819
1-3/M82	0.96277	1
2-1-1/M82	1.08118	0.764
2-1/M82	0.99298
2-6/M82	1.1496	0.695
3-2/M82	0.97258	1
4-1-1/M82	1.04139	1
4-1/M82	1.33712
4-3-2/M82	1.04587
4-3/M82	0.97109	1
5-3/M82	0.98011	1
6-2/M82	0.81424	0.497
6-3/M82	1.07144
7-1/M82	1.20958
7-2/M82	0.79235
9-3-2/M82	0.95551	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08952	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95426	1
IL12-4/WTpooled	1.0786	0.673
IL1-4/WTpooled	0.87624
WT/WTpooled	0.98525	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	0.91635	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09231	0.724
DC3000/delta hrp 6h	1.36655	1
DC3000/delta hrp 12h	0.70239	1
DC3000/delta hrp 24h	1.82083	0.051

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10681	0.29
DC3000 delta B/DC3000 delta AB	0.97066	0.805

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06615	1
Exp 36h	0.67022	0.406
Exp 60h	0.84043	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98646	1
Var 0h	0.81547	0.237
Var 12h I row2-row1	1.20061	0.242
Var 12h NI row2-row1	0.77233	0.438
Var 36h I row2-row1	1.10608	1
Var 36h NI row2-row1	1.0818	1
Var 60h I row2-row1	1.03116	1
Var 60h NI row2-row1	1.05816	0.904
Time course 0hI-0hNI	1.01216	1
Time course 12hI-12hNI	0.86965	0.166
Time course 36hI-36hNI	0.82893	0.032
Time course 60hI-60hNI	0.60519	0.006

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)	0.91724	0.377
transgenic ySAMdc/azygous control (breaker)	0.66633	0.137
transgenic ySAMdc/azygous control (red)	0.86243	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03507	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37034	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96861	1
Manapal/WT (break)	0.81169	0.333
Manapal/WT (red)	0.82625	0.181