Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.15.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04833	0.851
27DAP/17DAP	1.08926	0.86
39DAP/27DAP	1.04454	1
41DAP/39DAP	1.3069	0.535
42DAP/41DAP	0.83848	0.774
43DAP/42DAP	0.92742	0.705
47DAP/43DAP	1.04523	0.95
52DAP/47DAP	1.0808	0.949
57DAP/52DAP	0.98729	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9698	0.476
17DAP/reference	0.95524	0.342
27DAP/reference	1.00825	1
39DAP/reference	0.99197	0.874
41DAP/reference	1.04425	0.158
42DAP/reference	0.97278	0.169
43DAP/reference	0.93484	0.093
47DAP/reference	0.96427	0.098
52DAP/reference	1.08014	0.663
57DAP/reference	1.06293	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02691	0.785
27DAP/17DAP	1.01152	0.969
39DAP/27DAP	1.04007	0.615
41DAP/39DAP	1.03635	0.909
42DAP/41DAP	0.9973	0.91
43DAP/42DAP	1.00403	0.83
47DAP/43DAP	1.08367	0.221
52DAP/47DAP	0.98701	0.93
57DAP/52DAP	0.92681	0.221
57DAP/7DAP	1.0487	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94287	0.115
17DAP/reference	0.93312	0.021
27DAP/reference	0.92449	0.017
39DAP/reference	1.00089	1
41DAP/reference	0.98772	0.469
42DAP/reference	0.97969	0.371
43DAP/reference	0.94787	0.037
47DAP/reference	0.95029	0.128
52DAP/reference	0.91839	0.043
57DAP/reference	0.95573	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92341	0.306
17DAP/reference	1.00505	1
27DAP/reference	0.91609	0.144
39DAP/reference	0.98687	0.539
41DAP/reference	0.90912	0.188
42DAP/reference	0.96726	0.392
43DAP/reference	0.94562	0.292
47DAP/reference	0.91945	0.017
52DAP/reference	0.98099	0.302
57DAP/reference	0.89852	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97333	0.119
17DAP/reference	0.96119	0.389
27DAP/reference	0.96417	0.243
39DAP/reference	0.93725	0.012
41DAP/reference	0.98831	0.682
42DAP/reference	0.89084	0.049
43DAP/reference	0.97564	0.523
47DAP/reference	0.98114	0.452
52DAP/reference	0.8789	0.144
57DAP/reference	1.12347	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99796	1
26DAP/20DAP	0.93821	1
34DAP/26DAP	0.96588	0.803
51DAP/34DAP	1.04253	0.869
52DAP/51DAP	1.00924	0.888
53DAP/52DAP	1.04625	0.901
55DAP/53DAP	0.9042	0.417
57DAP/55DAP	1.05413	0.854
62DAP/57DAP	1.10628	0.257
68DAP/62DAP	0.95384	0.769
68DAP/14DAP	1.09931	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02648	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.87726	0.226
Immature Eggplant/Mature Eggplant	1.39564
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.38795

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99215	1
1-1-2/M82	1.02496	1
12-2/M82	0.99377	1
12-4/M82	0.94106	1
1-3/M82	0.97218	1
2-1-1/M82	1.01863	1
2-1/M82	1.27286
2-6/M82	0.94157	1
3-2/M82	1.08353	0.388
4-1-1/M82	0.99113	1
4-1/M82	0.88442	0.737
4-3-2/M82	0.85495	0.487
4-3/M82	1.01801	1
5-3/M82	0.99834	1
6-2/M82	1.00561	1
6-3/M82	1.05333	1
7-1/M82	1.18706	0.598
7-2/M82	1.04826	1
9-3-2/M82	0.79401	0.355

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	1.46796	0.362
IL12-4/WTpooled	1.45182	0.595
IL1-4/WTpooled	0.89044	0.699
WT/WTpooled	1.13785	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08665	0.692
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.74039	1
DC3000/delta hrp 24h	1.01287	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09794	0.16
DC3000 delta B/DC3000 delta AB	1.05641	0.498

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95795	1
Var 0h	1.25934	0.98
Var 12h I row2-row1	1.16535	0.235
Var 12h NI row2-row1	1.04322	1
Var 36h I row2-row1	0.87294	1
Var 36h NI row2-row1	0.94168	0.743
Var 60h I row2-row1	1.29135	1
Var 60h NI row2-row1	1.00859	1
Time course 0hI-0hNI	1.09364	0.719
Time course 12hI-12hNI	1.0039	1
Time course 36hI-36hNI	0.92784	0.255
Time course 60hI-60hNI	1.10269	0.137

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)	1.28984	0.748
transgenic ySAMdc/azygous control (breaker)	1.60494	0.248
transgenic ySAMdc/azygous control (red)	1.25719	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0101	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04655	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85533	0.172
Manapal/WT (break)	1.04007	1
Manapal/WT (red)	1.04109	1