Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01593	0.919
27DAP/17DAP	0.9529	0.877
39DAP/27DAP	1.14006	0.755
41DAP/39DAP	1.03542	0.919
42DAP/41DAP	0.78696	0.774
43DAP/42DAP	0.98193	0.93
47DAP/43DAP	0.94518	0.768
52DAP/47DAP	1.05815	0.898
57DAP/52DAP	1.0088	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01688	0.928
17DAP/reference	1.012	0.631
27DAP/reference	1.01411	0.847
39DAP/reference	1.02352	0.114
41DAP/reference	1.05547	0.241
42DAP/reference	0.95941	0.035
43DAP/reference	1.04575	0.403
47DAP/reference	0.98306	0.392
52DAP/reference	0.97668	0.489
57DAP/reference	0.97138	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25779	0.508
27DAP/17DAP	1.52331	0.071
39DAP/27DAP	0.69883	0.161
41DAP/39DAP	1.28089	0.362
42DAP/41DAP	0.96706	0.708
43DAP/42DAP	0.93895	0.538
47DAP/43DAP	1.05109	0.985
52DAP/47DAP	0.96425	0.884
57DAP/52DAP	1.49975	0.042
57DAP/7DAP	0.70263	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90292	0.402
17DAP/reference	0.90627	0.253
27DAP/reference	0.96181	0.494
39DAP/reference	1.03588	1
41DAP/reference	0.92355	0.094
42DAP/reference	0.8842	0.144
43DAP/reference	1.1069	0.408
47DAP/reference	0.96815	0.504
52DAP/reference	1.17311	0.171
57DAP/reference	1.20756	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96726	0.655
17DAP/reference	0.97286	0.326
27DAP/reference	0.97209	0.438
39DAP/reference	0.99349	0.642
41DAP/reference	0.92952	0.13
42DAP/reference	0.95755	0.212
43DAP/reference	1.05541	0.515
47DAP/reference	0.9804	0.359
52DAP/reference	1.0357	0.3
57DAP/reference	0.9985	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00977	0.75
17DAP/reference	0.91245	0.47
27DAP/reference	1.08578	0.621
39DAP/reference	1.29556	0.035
41DAP/reference	1.18228	1
42DAP/reference	1.11258	0.818
43DAP/reference	1.12208	0.515
47DAP/reference	0.99282	0.626
52DAP/reference	1.24366	0.398
57DAP/reference	1.0895	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00025	1
26DAP/20DAP	1.77766	0.152
34DAP/26DAP	0.68944	0.153
51DAP/34DAP	0.86189	0.317
52DAP/51DAP	1.12715	0.776
53DAP/52DAP	0.75185	0.489
55DAP/53DAP	0.99803	0.864
57DAP/55DAP	1.10098	0.906
62DAP/57DAP	0.93773	0.994
68DAP/62DAP	0.95149	0.747
68DAP/14DAP	1.16897	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21954	0.064

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13076	0.666
Mature Green Tomato/Ripe Tomato	1.11222	0.363
Immature Eggplant/Mature Eggplant	1.04061	0.528
Ripe Pepper/Ripe Tomato	0.66098	0.293
Mature Eggplant/Ripe Tomato	1.13776	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.71016
12-2/M82	N/A	N/A
12-4/M82	0.98435	1
1-3/M82	N/A	N/A
2-1-1/M82	0.93093
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.24245
4-1-1/M82	N/A	N/A
4-1/M82	1.14628
4-3-2/M82	0.87453	1
4-3/M82	1.38511
5-3/M82	1.12487
6-2/M82	N/A	N/A
6-3/M82	0.96704
7-1/M82	1.23741
7-2/M82	1.14223	0.385
9-3-2/M82	0.93346	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63241	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.68459
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.10819	0.737
IL1-4/WTpooled	1.0355
WT/WTpooled	N/A	N/A

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	1.39625	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98346	1
DC3000/delta hrp 6h	0.97544	0.95
DC3000/delta hrp 12h	1.05505	1
DC3000/delta hrp 24h	0.96962	0.75

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16458	0.229
DC3000 delta B/DC3000 delta AB	0.96996	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98507	1
Exp 36h	1.2201	1
Exp 60h	1.11128	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02851	1
Var 0h	0.99984	1
Var 12h I row2-row1	1.01339	1
Var 12h NI row2-row1	1.22601	0.649
Var 36h I row2-row1	0.77374	0.805
Var 36h NI row2-row1	1.00015	1
Var 60h I row2-row1	0.7302	0.374
Var 60h NI row2-row1	1.26066	0.904
Time course 0hI-0hNI	1.05651	0.799
Time course 12hI-12hNI	0.90848	0.157
Time course 36hI-36hNI	0.85616	0.067
Time course 60hI-60hNI	0.96917	0.646

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)	1.0377	0.384
transgenic ySAMdc/azygous control (breaker)	1.43801	0.172
transgenic ySAMdc/azygous control (red)	1.061	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97904	0.263

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97018	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85488	1
Manapal/WT (break)	0.77283	0.333
Manapal/WT (red)	1.06546	1