Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.13.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94504	0.652
27DAP/17DAP	1.01683	0.966
39DAP/27DAP	1.03173	0.782
41DAP/39DAP	1.16243	0.753
42DAP/41DAP	1.02312	0.999
43DAP/42DAP	1.05388	1
47DAP/43DAP	1.06053	0.943
52DAP/47DAP	1.05886	0.875
57DAP/52DAP	0.80177	0.74

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90165	0.162
17DAP/reference	0.97141	0.597
27DAP/reference	1.06238	0.239
39DAP/reference	1.15445	0.352
41DAP/reference	1.06373	0.48
42DAP/reference	0.9934	0.531
43DAP/reference	1.00293	0.942
47DAP/reference	0.8854	0.065
52DAP/reference	0.88166	0.167
57DAP/reference	0.98151	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91775	0.484
27DAP/17DAP	1.14083	0.511
39DAP/27DAP	1.14013	0.353
41DAP/39DAP	0.76151	0.069
42DAP/41DAP	1.0361	1
43DAP/42DAP	1.54884	0.015
47DAP/43DAP	1.10761	0.95
52DAP/47DAP	0.90002	0.314
57DAP/52DAP	0.93095	0.28
57DAP/7DAP	1.07228	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06163	0.676
17DAP/reference	0.88108	0.167
27DAP/reference	0.95839	0.348
39DAP/reference	1.07126	0.436
41DAP/reference	1.13656	0.325
42DAP/reference	0.82779	0.09
43DAP/reference	1.05558	0.432
47DAP/reference	1.03062	0.868
52DAP/reference	0.96416	0.435
57DAP/reference	0.97717	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26815	0.073
17DAP/reference	1.00576	0.873
27DAP/reference	0.98402	0.554
39DAP/reference	0.81599	0.008
41DAP/reference	0.91989	0.173
42DAP/reference	1.02966	0.723
43DAP/reference	1.33517	0.297
47DAP/reference	1.07869	0.311
52DAP/reference	1.01215	1
57DAP/reference	0.98182	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07262	0.882
17DAP/reference	1.07628	0.612
27DAP/reference	0.96977	0.465
39DAP/reference	0.9995	0.889
41DAP/reference	1.04331	0.939
42DAP/reference	1.02968	0.716
43DAP/reference	0.94653	0.449
47DAP/reference	1.20778	0.133
52DAP/reference	0.97572	0.69
57DAP/reference	0.93224	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0274	1
26DAP/20DAP	0.85168	0.244
34DAP/26DAP	1.14215	0.819
51DAP/34DAP	1.20593	0.126
52DAP/51DAP	1.06706	0.939
53DAP/52DAP	1.41239	0.064
55DAP/53DAP	1.11956	0.689
57DAP/55DAP	0.82947	0.225
62DAP/57DAP	0.39589	0.002
68DAP/62DAP	1.22866	0.7
68DAP/14DAP	0.95692	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13564	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72361	0.132
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.93036	1
Mature Eggplant/Ripe Tomato	0.40786	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1535	0.591
1-1-2/M82	0.94072
12-2/M82	1.21616	0.61
12-4/M82	1.25889	1
1-3/M82	0.65299
2-1-1/M82	1.00836
2-1/M82	N/A	N/A
2-6/M82	1.09516	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.07968
4-1/M82	1.51705
4-3-2/M82	1.13421
4-3/M82	N/A	N/A
5-3/M82	0.99634	1
6-2/M82	0.68964
6-3/M82	0.93662	1
7-1/M82	N/A	N/A
7-2/M82	0.92707	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	N/A	N/A
IL2-6/WTpooled	1.4689	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83578	0.31
IL12-4/WTpooled	1.01215	1
IL1-4/WTpooled	1.28757
WT/WTpooled	1.02126	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	0.91015	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0695	0.921
DC3000/delta hrp 6h	1.02424	0.95
DC3000/delta hrp 12h	1.08909	1
DC3000/delta hrp 24h	1.27595	0.082

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17858	0.063
DC3000 delta B/DC3000 delta AB	1.0526	0.625

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.05338	1
Exp 60h	1.25975	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04266	1
Var 0h	1.04071	1
Var 12h I row2-row1	1.06163	0.406
Var 12h NI row2-row1	0.97062	0.906
Var 36h I row2-row1	1.08192	1
Var 36h NI row2-row1	0.86687	0.645
Var 60h I row2-row1	0.78684	0.287
Var 60h NI row2-row1	0.9429	1
Time course 0hI-0hNI	1.04054	0.799
Time course 12hI-12hNI	1.07517	0.197
Time course 36hI-36hNI	1.10075	0.248
Time course 60hI-60hNI	1.55302	0.009

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)	0.99394	0.862
transgenic ySAMdc/azygous control (breaker)	0.68127	0.15
transgenic ySAMdc/azygous control (red)	1.4431	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97841	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99185	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.09881	0.083
Manapal/WT (break)	1.51763	0.381
Manapal/WT (red)	1.33991	0.413