Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87833	0.436
27DAP/17DAP	0.96968	0.967
39DAP/27DAP	0.8177	0.39
41DAP/39DAP	1.06935	0.663
42DAP/41DAP	1.08199	0.941
43DAP/42DAP	1.02415	1
47DAP/43DAP	1.00297	0.943
52DAP/47DAP	1.0611	0.946
57DAP/52DAP	1.03775	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90707	0.205
17DAP/reference	0.96661	0.536
27DAP/reference	1.05126	0.548
39DAP/reference	0.96238	0.587
41DAP/reference	0.82209	0.114
42DAP/reference	0.91257	0.011
43DAP/reference	0.99369	0.82
47DAP/reference	1.13579	0.081
52DAP/reference	1.04692	0.766
57DAP/reference	1.12851	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96564	0.595
27DAP/17DAP	0.97924	0.887
39DAP/27DAP	0.98637	0.898
41DAP/39DAP	1.01087	0.883
42DAP/41DAP	1.03361	0.763
43DAP/42DAP	1.03845	0.25
47DAP/43DAP	1.01403	0.914
52DAP/47DAP	1.04129	0.823
57DAP/52DAP	0.96703	0.603
57DAP/7DAP	0.98351	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55817	0.033
17DAP/reference	1.32556	0.028
27DAP/reference	1.17782	0.041
39DAP/reference	2.07487	0.005
41DAP/reference	1.41995	0.011
42DAP/reference	1.70393	0.007
43DAP/reference	1.52059	0.007
47DAP/reference	1.50899	0.019
52DAP/reference	1.82935	0.008
57DAP/reference	1.71472	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91336	0.231
17DAP/reference	0.83629	0.047
27DAP/reference	1.05372	1
39DAP/reference	1.11429	0.389
41DAP/reference	1.07479	0.471
42DAP/reference	1.04854	0.715
43DAP/reference	0.96285	0.438
47DAP/reference	1.10198	0.4
52DAP/reference	0.89088	0.043
57DAP/reference	0.8424	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25428	0.04
17DAP/reference	1.02528	0.886
27DAP/reference	1.14687	0.227
39DAP/reference	1.23395	0.022
41DAP/reference	1.16433	0.039
42DAP/reference	1.19032	0.127
43DAP/reference	1.40373	0.077
47DAP/reference	1.05328	1
52DAP/reference	1.36235	0.172
57DAP/reference	2.10988	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95838	1
26DAP/20DAP	1.00062	1
34DAP/26DAP	0.92563
51DAP/34DAP	1.03106	0.814
52DAP/51DAP	1.0338	0.758
53DAP/52DAP	0.95334	0.783
55DAP/53DAP	0.94164	0.592
57DAP/55DAP	0.9626	0.821
62DAP/57DAP	1.46648	0.35
68DAP/62DAP	2.34636	0.029
68DAP/14DAP	1.86849	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06086	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.72915	0.058
Mature Green Tomato/Ripe Tomato	1.1969	0.267
Immature Eggplant/Mature Eggplant	0.98275	0.651
Ripe Pepper/Ripe Tomato	0.5156	0.293
Mature Eggplant/Ripe Tomato	0.73122	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8265	0.708
1-1-2/M82	1.15783	0.977
12-2/M82	0.88146	0.955
12-4/M82	1.10424
1-3/M82	1.05747	1
2-1-1/M82	N/A	N/A
2-1/M82	0.99914
2-6/M82	0.79626	1
3-2/M82	1.19348
4-1-1/M82	0.57406
4-1/M82	1.26147
4-3-2/M82	0.82304	0.487
4-3/M82	1.09951	1
5-3/M82	1.10643	1
6-2/M82	0.86202
6-3/M82	N/A	N/A
7-1/M82	1.00229	1
7-2/M82	1.09262	1
9-3-2/M82	0.69207	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9306	1
IL2-6/WTpooled	1.08793	0.659
IL7-5/WTpooled	0.90502	1
IL7-3/WTpooled	1.2449	1
IL12-4/WTpooled	0.84346	0.581
IL1-4/WTpooled	0.96063	0.834
WT/WTpooled	1.01293	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	0.89917	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98742	1
DC3000/delta hrp 6h	1.40421	0.978
DC3000/delta hrp 12h	0.93098	1
DC3000/delta hrp 24h	0.89995	0.338

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26015	0.048
DC3000 delta B/DC3000 delta AB	1.2018	0.175

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90873	1
Exp 36h	0.81171	0.589
Exp 60h	0.77371	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9871	1
Var 0h	0.91015	1
Var 12h I row2-row1	1.18471	0.222
Var 12h NI row2-row1	1.03077	1
Var 36h I row2-row1	1.05821	1
Var 36h NI row2-row1	0.96954	0.791
Var 60h I row2-row1	1.06737	1
Var 60h NI row2-row1	1.09424	0.904
Time course 0hI-0hNI	1.01622	1
Time course 12hI-12hNI	1.00564	1
Time course 36hI-36hNI	1.00034	0.798
Time course 60hI-60hNI	1.21603	0.096

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)	1.08626	0.431
transgenic ySAMdc/azygous control (breaker)	1.0031	1
transgenic ySAMdc/azygous control (red)	0.85021	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02861	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2302	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.66167	0.088
Manapal/WT (break)	1.17798	0.13
Manapal/WT (red)	1.83591	0.164