Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.15.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.87395	0.096
27DAP/17DAP	0.66877	0.157
39DAP/27DAP	1.10385	0.755
41DAP/39DAP	0.77085	0.177
42DAP/41DAP	0.77382	0.774
43DAP/42DAP	0.77259	0.627
47DAP/43DAP	0.94593	0.724
52DAP/47DAP	0.80766	0.526
57DAP/52DAP	1.08642	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29476	0.032
17DAP/reference	1.49273	0.112
27DAP/reference	1.24222	0.025
39DAP/reference	1.13566	0.603
41DAP/reference	1.64729	0.014
42DAP/reference	0.8212	0.009
43DAP/reference	0.76481	0.039
47DAP/reference	0.72466	0.003
52DAP/reference	0.9332	0.33
57DAP/reference	0.73388	0.033

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1231	0.749
27DAP/17DAP	1.18802	0.287
39DAP/27DAP	0.67676	0.066
41DAP/39DAP	1.5721	0.051
42DAP/41DAP	0.8533	0.179
43DAP/42DAP	0.57217	0.034
47DAP/43DAP	1.01673	0.906
52DAP/47DAP	1.37847	0.471
57DAP/52DAP	1.13998	0.978
57DAP/7DAP	0.97628	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07205	0.613
17DAP/reference	0.77011	0.012
27DAP/reference	0.81	0.019
39DAP/reference	1.24624	0.12
41DAP/reference	0.74336	0.021
42DAP/reference	0.74113	0.013
43DAP/reference	0.5794	0.011
47DAP/reference	0.63545	0.044
52DAP/reference	0.64105	0.012
57DAP/reference	0.57951	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06255	0.634
17DAP/reference	1.24013	0.426
27DAP/reference	1.16625	0.404
39DAP/reference	1.5877	0.015
41DAP/reference	0.9466	0.348
42DAP/reference	0.94866	0.392
43DAP/reference	0.84512	0.25
47DAP/reference	0.9973	0.59
52DAP/reference	0.95594	0.327
57DAP/reference	0.63027	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84747	0.214
17DAP/reference	0.96733	0.615
27DAP/reference	0.75682	0.041
39DAP/reference	0.83228	0.031
41DAP/reference	0.70271	0.023
42DAP/reference	0.65773	0.015
43DAP/reference	0.71791	0.023
47DAP/reference	0.69839	0.025
52DAP/reference	0.67987	0.119
57DAP/reference	0.9749	0.5

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9457	1
26DAP/20DAP	1.18012	1
34DAP/26DAP	0.76261	0.343
51DAP/34DAP	1.02674	0.901
52DAP/51DAP	0.83898	1
53DAP/52DAP	2.18277	0.07
55DAP/53DAP	1.44777	0.634
57DAP/55DAP	0.87362	0.587
62DAP/57DAP	0.96576	0.994
68DAP/62DAP	1.44433
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32395	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	15.7387	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.15675

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.74423	0.613
1-1-2/M82	0.5051
12-2/M82	N/A	N/A
12-4/M82	0.39308	0.298
1-3/M82	0.30618
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.5485
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.68005
4-3-2/M82	1.40514
4-3/M82	N/A	N/A
5-3/M82	0.86369	1
6-2/M82	N/A	N/A
6-3/M82	0.51575
7-1/M82	0.84309
7-2/M82	0.81727
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13374	1
IL12-4/WTpooled	0.94562	1
IL1-4/WTpooled	1.0643	1
WT/WTpooled	1.13818

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	1.03992	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96519	1
DC3000/delta hrp 6h	1.11538	1
DC3000/delta hrp 12h	1.28324	1
DC3000/delta hrp 24h	0.82798	0.274

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.48632
DC3000 delta B/DC3000 delta AB	0.63332	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0788	1
Exp 36h	0.37301	0.471
Exp 60h	0.47035	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02074	1
Var 0h	0.70809	1
Var 12h I row2-row1	0.5963	0.357
Var 12h NI row2-row1	0.86489	0.546
Var 36h I row2-row1	0.92095	0.805
Var 36h NI row2-row1	1.29362	0.482
Var 60h I row2-row1	1.08733	1
Var 60h NI row2-row1	0.96307	1
Time course 0hI-0hNI	0.99898	1
Time course 12hI-12hNI	0.9352	0.476
Time course 36hI-36hNI	0.79803	0.03
Time course 60hI-60hNI	0.10929	0.006

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)	0.93545	0.567
transgenic ySAMdc/azygous control (breaker)	1.6878	0.162
transgenic ySAMdc/azygous control (red)	1.03492	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.88185	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.8618	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.3148	0.307
Manapal/WT (break)	1.51872	0.381
Manapal/WT (red)	0.77673	0.36