Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.6.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65057	0.128
27DAP/17DAP	0.83706	0.585
39DAP/27DAP	1.43933	0.277
41DAP/39DAP	1.16071	0.797
42DAP/41DAP	1.32697	0.449
43DAP/42DAP	1.13274	1
47DAP/43DAP	1.1983	0.733
52DAP/47DAP	0.91114	0.72
57DAP/52DAP	1.42389	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43723	0.018
17DAP/reference	1.04377	0.74
27DAP/reference	0.93678	0.075
39DAP/reference	0.99483	0.901
41DAP/reference	1.15533	0.287
42DAP/reference	1.38672	0.001
43DAP/reference	1.21353	0.064
47DAP/reference	1.30721	0.001
52DAP/reference	0.80074	0.021
57DAP/reference	0.9155	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87541	0.238
27DAP/17DAP	1.34956	0.067
39DAP/27DAP	0.925	0.556
41DAP/39DAP	1.00443	1
42DAP/41DAP	1.12263	0.593
43DAP/42DAP	1.19107	0.212
47DAP/43DAP	0.99773	0.989
52DAP/47DAP	0.94328	0.797
57DAP/52DAP	1.26692	0.23
57DAP/7DAP	0.71923	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.46357	0.106
17DAP/reference	0.95116	0.518
27DAP/reference	0.71874	0.082
39DAP/reference	0.98659	0.552
41DAP/reference	1.21728	0.812
42DAP/reference	0.84972	0.211
43DAP/reference	0.96573	0.459
47DAP/reference	1.11644	0.386
52DAP/reference	1.03119	0.74
57DAP/reference	0.99029	0.61

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40675	0.258
17DAP/reference	1.57848	0.009
27DAP/reference	1.11373	0.535
39DAP/reference	1.04404	0.912
41DAP/reference	1.01636	0.735
42DAP/reference	1.26935	0.014
43DAP/reference	1.02087	0.801
47DAP/reference	1.08381	0.454
52DAP/reference	1.03168	0.938
57DAP/reference	0.77814	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04752	1
17DAP/reference	1.51853	0.206
27DAP/reference	1.05217
39DAP/reference	0.92832	0.504
41DAP/reference	1.26217	0.867
42DAP/reference	1.76307	0.013
43DAP/reference	1.40307	0.403
47DAP/reference	0.93839	0.335
52DAP/reference	0.83604	0.16
57DAP/reference	0.81596	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97522	1
26DAP/20DAP	1.29063	0.293
34DAP/26DAP	0.98403	0.98
51DAP/34DAP	1.31395	0.185
52DAP/51DAP	1.15965	0.733
53DAP/52DAP	1.33173	0.058
55DAP/53DAP	0.74987	0.033
57DAP/55DAP	1.30309	0.348
62DAP/57DAP	1.17452	0.069
68DAP/62DAP	0.95499	0.834
68DAP/14DAP	1.38752	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96895	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	28.7182	0.058
Mature Green Tomato/Ripe Tomato	0.82678	0.182
Immature Eggplant/Mature Eggplant	0.78709	0.159
Ripe Pepper/Ripe Tomato	0.54888	1
Mature Eggplant/Ripe Tomato	0.88971	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.23477	0.742
1-1-2/M82	0.77904	1
12-2/M82	1.54224
12-4/M82	1.1608	0.611
1-3/M82	N/A	N/A
2-1-1/M82	0.89073	1
2-1/M82	N/A	N/A
2-6/M82	0.79231	1
3-2/M82	0.97926
4-1-1/M82	0.93946
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.33215	0.268
5-3/M82	0.94408	1
6-2/M82	N/A	N/A
6-3/M82	1.05944	1
7-1/M82	0.9314	0.803
7-2/M82	0.78111	0.599
9-3-2/M82	1.29391

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01973	1
IL2-6/WTpooled	1.39544	0.531
IL7-5/WTpooled	0.82482	0.559
IL7-3/WTpooled	1.0851
IL12-4/WTpooled	0.87443	0.71
IL1-4/WTpooled	0.97203	0.834
WT/WTpooled	1.0282	0.686

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	1.17961	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98959	1
DC3000/delta hrp 6h	0.98169	0.95
DC3000/delta hrp 12h	1.36	1
DC3000/delta hrp 24h	1.07009	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63709
DC3000 delta B/DC3000 delta AB	1.23399	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81361	1
Exp 36h	1.01906	1
Exp 60h	1.0498	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01866	1
Var 0h	1.31929	0.782
Var 12h I row2-row1	1.24841	0.324
Var 12h NI row2-row1	0.88001	0.82
Var 36h I row2-row1	0.91733	0.805
Var 36h NI row2-row1	1.06758	1
Var 60h I row2-row1	0.62982	0.285
Var 60h NI row2-row1	1.19069	0.904
Time course 0hI-0hNI	0.97489	0.898
Time course 12hI-12hNI	1.09434	0.321
Time course 36hI-36hNI	1.21579	0.005
Time course 60hI-60hNI	2.34083	0.008

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)	1.20556	0.305
transgenic ySAMdc/azygous control (breaker)	1.10559	1
transgenic ySAMdc/azygous control (red)	0.94747	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02934	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23208	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.6234	0.14
Manapal/WT (break)	1.06834	1
Manapal/WT (red)	0.67749	0.181