Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9702	0.76
27DAP/17DAP	1.40311	0.677
39DAP/27DAP	0.86274	0.549
41DAP/39DAP	1.8548	0.323
42DAP/41DAP	0.99652	1
43DAP/42DAP	0.95374	0.895
47DAP/43DAP	0.85709	0.55
52DAP/47DAP	1.59225	0.215
57DAP/52DAP	0.94016	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24406	0.026
17DAP/reference	1.06297	0.528
27DAP/reference	0.95715	0.339
39DAP/reference	1.00531	1
41DAP/reference	1.09151	0.338
42DAP/reference	1.14823	0.033
43DAP/reference	1.05537	0.403
47DAP/reference	1.11073	0.154
52DAP/reference	0.98606	0.53
57DAP/reference	0.98324	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00388	0.871
27DAP/17DAP	1.09092	0.798
39DAP/27DAP	1.03685	0.742
41DAP/39DAP	0.99159	0.997
42DAP/41DAP	1.01892	1
43DAP/42DAP	1.15094	0.061
47DAP/43DAP	1.02568	0.939
52DAP/47DAP	0.9762	0.907
57DAP/52DAP	0.87515	0.219
57DAP/7DAP	1.38321	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9777	0.55
17DAP/reference	0.84581	0.013
27DAP/reference	0.87021	0.014
39DAP/reference	0.86485	0.049
41DAP/reference	0.88533	0.213
42DAP/reference	0.71938	N/A
43DAP/reference	0.76522	0.056
47DAP/reference	1.24906	0.43
52DAP/reference	0.8161	0.021
57DAP/reference	0.76002	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13459	0.463
17DAP/reference	1.0867	0.773
27DAP/reference	1.33636	0.166
39DAP/reference	1.30799	0.281
41DAP/reference	1.22512	0.096
42DAP/reference	1.3191	0.01
43DAP/reference	1.08618	0.605
47DAP/reference	1.20625	0.008
52DAP/reference	1.02873	0.988
57DAP/reference	0.99357	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82783	0.044
17DAP/reference	0.9227	0.224
27DAP/reference	0.81197	0.038
39DAP/reference	0.76473	0.009
41DAP/reference	0.97029	0.618
42DAP/reference	0.97422	0.671
43DAP/reference	0.89066	0.171
47DAP/reference	1.02795	1
52DAP/reference	1.01437	0.623
57DAP/reference	1.33699	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17007	0.966
26DAP/20DAP	0.85502	0.317
34DAP/26DAP	1.01622	1
51DAP/34DAP	1.05337	0.925
52DAP/51DAP	1.31706	0.154
53DAP/52DAP	1.01954	0.91
55DAP/53DAP	1.14387	0.519
57DAP/55DAP	1.14008	0.865
62DAP/57DAP	0.92282	0.871
68DAP/62DAP	1.94158	0.113
68DAP/14DAP	3.82625	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14008	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03186	1
Mature Green Tomato/Ripe Tomato	0.85316	0.287
Immature Eggplant/Mature Eggplant	1.19308	0.205
Ripe Pepper/Ripe Tomato	1.67482	0.256
Mature Eggplant/Ripe Tomato	1.47095	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02246	1
1-1-2/M82	0.88728	1
12-2/M82	1.34026	N/A
12-4/M82	0.8906	1
1-3/M82	1.01691	1
2-1-1/M82	1.13528	0.689
2-1/M82	N/A	N/A
2-6/M82	0.99823	1
3-2/M82	0.78894	N/A
4-1-1/M82	0.83984	N/A
4-1/M82	0.93578	1
4-3-2/M82	0.79662	0.698
4-3/M82	1.04372	N/A
5-3/M82	0.9751	1
6-2/M82	N/A	N/A
6-3/M82	0.95858	1
7-1/M82	N/A	N/A
7-2/M82	0.86809	0.881
9-3-2/M82	0.78877	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93112	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03624	1
IL12-4/WTpooled	1.3878	0.516
IL1-4/WTpooled	0.9561	0.834
WT/WTpooled	1.02176	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	1.06311	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94576	1
DC3000/delta hrp 6h	0.97728	0.95
DC3000/delta hrp 12h	0.95314	1
DC3000/delta hrp 24h	1.10282	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.00012	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87645	1
Exp 36h	1.84751	0.693
Exp 60h	1.43913	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98949	1
Var 0h	0.83828	0.933
Var 12h I row2-row1	1.06371	0.58
Var 12h NI row2-row1	0.89082	0.713
Var 36h I row2-row1	0.92852	1
Var 36h NI row2-row1	0.94426	0.706
Var 60h I row2-row1	1.4977	0.562
Var 60h NI row2-row1	1.35508	0.904
Time course 0hI-0hNI	1.09244	0.799
Time course 12hI-12hNI	1.04083	0.773
Time course 36hI-36hNI	0.92428	0.144
Time course 60hI-60hNI	1.07529	0.254

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)	1.11113	0.612
transgenic ySAMdc/azygous control (breaker)	0.60016	0.142
transgenic ySAMdc/azygous control (red)	1.12572	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0656	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79822	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13874	0.307
Manapal/WT (break)	1.22876	0.381
Manapal/WT (red)	1.13249	1