Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01819	0.919
27DAP/17DAP	1.61298	0.57
39DAP/27DAP	0.74494	0.487
41DAP/39DAP	1.22255	0.85
42DAP/41DAP	0.89384	1
43DAP/42DAP	0.96034	0.9
47DAP/43DAP	1.1095	0.633
52DAP/47DAP	1.2117	0.76
57DAP/52DAP	1.09922	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90152	0.097
17DAP/reference	0.97849	0.777
27DAP/reference	0.9172	0.304
39DAP/reference	0.84266	0.424
41DAP/reference	1.15507	0.365
42DAP/reference	1.08489	0.756
43DAP/reference	0.5524
47DAP/reference	1.06992	0.72
52DAP/reference	0.80946	0.046
57DAP/reference	0.43521

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78454	0.238
27DAP/17DAP	1.05714	1
39DAP/27DAP	1.0082	0.953
41DAP/39DAP	1.10102	0.827
42DAP/41DAP	1.42458	0.74
43DAP/42DAP	0.75033	0.028
47DAP/43DAP	1.17427	0.593
52DAP/47DAP	1.00723	0.919
57DAP/52DAP	0.78471	0.123
57DAP/7DAP	0.99356	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87771	0.168
17DAP/reference	0.88604	0.072
27DAP/reference	1.10865	0.049
39DAP/reference	0.70629	0.02
41DAP/reference	0.81121	0.031
42DAP/reference	0.73385	0.011
43DAP/reference	0.73478	0.029
47DAP/reference	0.86513	0.293
52DAP/reference	0.78485	0.053
57DAP/reference	0.9562	0.411

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19721	0.355
17DAP/reference	1.22787	0.367
27DAP/reference	1.05658	0.686
39DAP/reference	1.00605	1
41DAP/reference	1.33448	0.018
42DAP/reference	1.13203	0.655
43DAP/reference	1.65525	0.031
47DAP/reference	1.02677	1
52DAP/reference	1.08056	0.417
57DAP/reference	1.12183	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94467	0.391
17DAP/reference	1.10227	0.578
27DAP/reference	0.94842	0.397
39DAP/reference	0.89428	0.179
41DAP/reference	1.04363	0.939
42DAP/reference	1.0407	0.743
43DAP/reference	0.77538	0.076
47DAP/reference	1.09594	0.405
52DAP/reference	0.99135	0.838
57DAP/reference	0.96126	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99335	1
26DAP/20DAP	1.59476	0.143
34DAP/26DAP	0.66839	0.152
51DAP/34DAP	1.42525	0.032
52DAP/51DAP	0.88537	1
53DAP/52DAP	1.42836	0.565
55DAP/53DAP	0.85429	0.303
57DAP/55DAP	1.23357	0.51
62DAP/57DAP	1.36701	0.515
68DAP/62DAP	1.48032	0.052
68DAP/14DAP	1.73616	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74611	0.166

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68958	0.254
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.84008	0.72
Ripe Pepper/Ripe Tomato	0.68522	0.224
Mature Eggplant/Ripe Tomato	0.92643	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10536	0.551
1-1-2/M82	1.38848
12-2/M82	N/A	N/A
12-4/M82	1.33225
1-3/M82	0.59902
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.79352
4-1/M82	N/A	N/A
4-3-2/M82	0.85682
4-3/M82	1.12539
5-3/M82	0.9242	1
6-2/M82	0.70986
6-3/M82	1.10451	1
7-1/M82	N/A	N/A
7-2/M82	0.88698	0.881
9-3-2/M82	0.88708

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9595
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.29452
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.04201	0.839
IL1-4/WTpooled	0.87772
WT/WTpooled	1.19615

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	1.33566	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01195	1
DC3000/delta hrp 6h	1.5025	1
DC3000/delta hrp 12h	1.04795	1
DC3000/delta hrp 24h	1.26478	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05805
DC3000 delta B/DC3000 delta AB	1.09639	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79266	1
Exp 36h	1.09525	1
Exp 60h	0.84867	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0103	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.42858	0.324
Var 12h NI row2-row1	1.00168	1
Var 36h I row2-row1	0.94662	0.805
Var 36h NI row2-row1	0.77	0.706
Var 60h I row2-row1	0.98102	0.952
Var 60h NI row2-row1	0.88423	0.292
Time course 0hI-0hNI	0.83736	0.126
Time course 12hI-12hNI	0.85431	0.212
Time course 36hI-36hNI	0.8643	0.171
Time course 60hI-60hNI	1.1788	0.16

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)	1.93615	0.36
transgenic ySAMdc/azygous control (breaker)	0.89249	0.49
transgenic ySAMdc/azygous control (red)	1.31532	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98149	0.588

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82367	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97989	1
Manapal/WT (break)	1.02082	1
Manapal/WT (red)	0.82094	0.181