Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.14387	0.033
27DAP/17DAP	0.76125	0.312
39DAP/27DAP	1.10307	0.915
41DAP/39DAP	0.85036	0.445
42DAP/41DAP	1.45248	0.477
43DAP/42DAP	1.26221	0.869
47DAP/43DAP	0.93139	0.716
52DAP/47DAP	0.65194	0.174
57DAP/52DAP	0.91837	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19553	0.35
17DAP/reference	1.31789	0.161
27DAP/reference	1.18426	0.221
39DAP/reference	1.50342	0.026
41DAP/reference	1.20963	0.241
42DAP/reference	1.37911	0.001
43DAP/reference	1.52103	0.008
47DAP/reference	1.85633	0.001
52DAP/reference	1.08384	0.354
57DAP/reference	1.19192	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46191	0.036
27DAP/17DAP	0.72777	0.091
39DAP/27DAP	0.87976	0.304
41DAP/39DAP	1.5697	0.012
42DAP/41DAP	0.91635	0.384
43DAP/42DAP	0.99726	1
47DAP/43DAP	1.06277	0.61
52DAP/47DAP	1.07328	0.734
57DAP/52DAP	0.64062	0.063
57DAP/7DAP	0.93387	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24789	0.039
17DAP/reference	1.65464	0.009
27DAP/reference	1.37375	0.008
39DAP/reference	1.25982	0.03
41DAP/reference	1.7198	0.009
42DAP/reference	1.53693	0.008
43DAP/reference	1.7013	0.008
47DAP/reference	1.73573	0.019
52DAP/reference	1.30038	0.031
57DAP/reference	1.38481	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98013	0.688
17DAP/reference	1.94218	0.007
27DAP/reference	1.65654	0.063
39DAP/reference	1.19948	0.247
41DAP/reference	1.65729	0.005
42DAP/reference	1.36253	0.008
43DAP/reference	1.30934	0.211
47DAP/reference	1.92436	0.008
52DAP/reference	1.03606	0.789
57DAP/reference	1.03954	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06588	0.303
17DAP/reference	1.59118	0.109
27DAP/reference	1.0159	1
39DAP/reference	1.40022	0.007
41DAP/reference	1.3481	0.02
42DAP/reference	1.71388	0.006
43DAP/reference	1.92132	0.009
47DAP/reference	1.81654	0.008
52DAP/reference	1.37994	0.082
57DAP/reference	1.36108	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15882	0.966
26DAP/20DAP	1.16933	1
34DAP/26DAP	0.8657	0.735
51DAP/34DAP	0.88106	0.532
52DAP/51DAP	0.92919	1
53DAP/52DAP	1.18676	0.384
55DAP/53DAP	0.85786	0.43
57DAP/55DAP	1.28577	0.118
62DAP/57DAP	0.97491	0.994
68DAP/62DAP	0.89084	0.609
68DAP/14DAP	0.99633	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.4842	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89799	0.436
Mature Green Tomato/Ripe Tomato	1.04188	0.948
Immature Eggplant/Mature Eggplant	0.47199	0.064
Ripe Pepper/Ripe Tomato	0.62502	0.224
Mature Eggplant/Ripe Tomato	0.38947	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.76417	0.536
1-1-2/M82	1.12904	1
12-2/M82	0.98992	1
12-4/M82	1.44165	1
1-3/M82	1.55427	0.479
2-1-1/M82	0.8917	1
2-1/M82	0.70957
2-6/M82	1.17428	0.385
3-2/M82	1.37429	0.84
4-1-1/M82	1.28051	1
4-1/M82	1.92129	1
4-3-2/M82	1.46366	0.246
4-3/M82	1.06343	1
5-3/M82	1.08441	1
6-2/M82	2.21654	0.253
6-3/M82	1.01148	1
7-1/M82	1.01725	1
7-2/M82	1.3898	0.385
9-3-2/M82	1.47438	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77503
IL2-6/WTpooled	0.93554	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83477	1
IL12-4/WTpooled	1.04495	1
IL1-4/WTpooled	0.85543
WT/WTpooled	1.07813	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	0.92358	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01538	0.921
DC3000/delta hrp 6h	1.02522	1
DC3000/delta hrp 12h	1.09308	1
DC3000/delta hrp 24h	0.78429	0.061

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10993	0.055
DC3000 delta B/DC3000 delta AB	1.22764	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92118	1
Exp 36h	1.24157	1
Exp 60h	0.87777	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00998	1
Var 0h	1.25385	0.274
Var 12h I row2-row1	0.84385	0.565
Var 12h NI row2-row1	1.21699	0.649
Var 36h I row2-row1	1.14409	1
Var 36h NI row2-row1	1.21314	1
Var 60h I row2-row1	0.92274	0.439
Var 60h NI row2-row1	0.88622	0.818
Time course 0hI-0hNI	0.99086	1
Time course 12hI-12hNI	0.98191	0.847
Time course 36hI-36hNI	0.99902	0.753
Time course 60hI-60hNI	0.981	0.646

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)	0.75926	0.255
transgenic ySAMdc/azygous control (breaker)	0.71873	0.139
transgenic ySAMdc/azygous control (red)	0.99024	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05636	0.234

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84726	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89082	1
Manapal/WT (break)	0.76288	0.333
Manapal/WT (red)	0.88792	0.424