Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43091	0.014
27DAP/17DAP	0.75733	0.32
39DAP/27DAP	0.83205	0.338
41DAP/39DAP	1.36851	0.363
42DAP/41DAP	0.95647	1
43DAP/42DAP	0.96491	0.892
47DAP/43DAP	1.09776	0.448
52DAP/47DAP	1.06497	0.949
57DAP/52DAP	1.06466	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15543	0.105
17DAP/reference	0.83296	0.028
27DAP/reference	0.77104	0.012
39DAP/reference	0.80787	0.031
41DAP/reference	0.82393	0.012
42DAP/reference	0.84866	0.001
43DAP/reference	0.83692	0.023
47DAP/reference	0.89386	0.016
52DAP/reference	0.8796	0.125
57DAP/reference	0.88641	0.021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8193	0.09
27DAP/17DAP	1.04828	0.842
39DAP/27DAP	0.95926	0.601
41DAP/39DAP	1.03945	0.883
42DAP/41DAP	0.98353	0.809
43DAP/42DAP	0.99071	0.928
47DAP/43DAP	0.96664	0.781
52DAP/47DAP	1.03375	0.883
57DAP/52DAP	0.94275	0.457
57DAP/7DAP	0.84577	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86396	0.054
17DAP/reference	0.91683	0.013
27DAP/reference	0.8734	0.01
39DAP/reference	0.90042	0.011
41DAP/reference	0.96978	0.469
42DAP/reference	0.9601	0.066
43DAP/reference	0.93446	0.079
47DAP/reference	0.69975	0.079
52DAP/reference	0.88799	0.043
57DAP/reference	0.95682	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16172	0.203
17DAP/reference	0.80477	0.003
27DAP/reference	0.83396	0.026
39DAP/reference	0.74876	0.042
41DAP/reference	0.90131	0.148
42DAP/reference	0.9242	0.321
43DAP/reference	0.71917	0.008
47DAP/reference	0.91346	0.066
52DAP/reference	0.71433	0.004
57DAP/reference	0.7526	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37552	0.024
17DAP/reference	0.89673	0.234
27DAP/reference	0.90685	0.05
39DAP/reference	0.92639	0.092
41DAP/reference	0.82435	0.05
42DAP/reference	0.78303	0.172
43DAP/reference	0.82476	0.037
47DAP/reference	0.64827	0.004
52DAP/reference	0.76754	0.087
57DAP/reference	0.78498	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05956	0.496
26DAP/20DAP	0.95128	1
34DAP/26DAP	0.93773	0.874
51DAP/34DAP	0.96422	0.747
52DAP/51DAP	1.03409	0.722
53DAP/52DAP	0.94969	0.803
55DAP/53DAP	1.02844	1
57DAP/55DAP	0.95871	0.774
62DAP/57DAP	1.82073	0.678
68DAP/62DAP	0.93229	0.668
68DAP/14DAP	1.00925	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94101	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.41849
Mature Green Tomato/Ripe Tomato	1.38944	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02001	1
1-1-2/M82	0.9466	1
12-2/M82	1.21192
12-4/M82	1.08713	1
1-3/M82	0.89593	0.501
2-1-1/M82	1.21246	0.689
2-1/M82	N/A	N/A
2-6/M82	1.02723	1
3-2/M82	1.05062
4-1-1/M82	1.15478
4-1/M82	1.03138	1
4-3-2/M82	0.8604	0.487
4-3/M82	1.05634	1
5-3/M82	0.97404	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.98513
7-2/M82	1.01453	1
9-3-2/M82	0.85555	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21961	0.46
IL7-5/WTpooled	1.8656
IL7-3/WTpooled	0.95882	1
IL12-4/WTpooled	0.93152
IL1-4/WTpooled	1.07574	1
WT/WTpooled	0.99939	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	0.75024	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98484	1
DC3000/delta hrp 6h	1.16626	1
DC3000/delta hrp 12h	0.88858	1
DC3000/delta hrp 24h	1.47017	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27631	0.042
DC3000 delta B/DC3000 delta AB	0.98413	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89807	1
Exp 36h	1.1164	0.943
Exp 60h	0.53846	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92284	1
Var 0h	1.09677	0.98
Var 12h I row2-row1	1.12351	0.196
Var 12h NI row2-row1	1.03615	1
Var 36h I row2-row1	0.99901	1
Var 36h NI row2-row1	0.95443	0.645
Var 60h I row2-row1	1.08632	1
Var 60h NI row2-row1	0.94613	0.866
Time course 0hI-0hNI	1.03333	0.852
Time course 12hI-12hNI	1.03965	0.747
Time course 36hI-36hNI	0.98997	0.654
Time course 60hI-60hNI	0.98896	1

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)	0.94586	0.567
transgenic ySAMdc/azygous control (breaker)	1.39041	0.178
transgenic ySAMdc/azygous control (red)	1.02829	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02211	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98644	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.29519	0.086
Manapal/WT (break)	0.92613	1
Manapal/WT (red)	0.78749	0.184