Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.25954	0.07
27DAP/17DAP	2.00878	0.353
39DAP/27DAP	1.28409	0.759
41DAP/39DAP	0.91112	0.536
42DAP/41DAP	1.15385	0.903
43DAP/42DAP	1.40247	0.47
47DAP/43DAP	1.28101	0.776
52DAP/47DAP	0.79915	0.502
57DAP/52DAP	1.48215	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89947	0.177
17DAP/reference	0.98409	0.737
27DAP/reference	1.01321	1
39DAP/reference	1.11479	0.413
41DAP/reference	0.9678	0.542
42DAP/reference	0.83398	0.075
43DAP/reference	1.01205	1
47DAP/reference	0.90686	0.106
52DAP/reference	0.94418	0.31
57DAP/reference	0.909	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02572	0.899
27DAP/17DAP	1.13273	0.639
39DAP/27DAP	1.07372	0.646
41DAP/39DAP	1.10068	0.853
42DAP/41DAP	0.96208	0.737
43DAP/42DAP	1.08377	0.699
47DAP/43DAP	1.0089	1
52DAP/47DAP	1.0887	0.724
57DAP/52DAP	0.86816	0.451
57DAP/7DAP	1.27759	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86275	0.073
17DAP/reference	0.87965	0.049
27DAP/reference	0.90401	0.076
39DAP/reference	0.87157	0.064
41DAP/reference	0.78166	0.031
42DAP/reference	0.71821	0.01
43DAP/reference	0.77016	0.013
47DAP/reference	0.91842	0.293
52DAP/reference	0.75884	0.014
57DAP/reference	0.76093	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11709	0.36
17DAP/reference	1.14605	0.531
27DAP/reference	1.05313	0.847
39DAP/reference	0.87876	0.168
41DAP/reference	0.9416	0.364
42DAP/reference	0.92332	0.321
43DAP/reference	1.68601	0.014
47DAP/reference	0.99708	0.73
52DAP/reference	1.00221	0.666
57DAP/reference	1.25819	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92513	0.362
17DAP/reference	1.02281	1
27DAP/reference	0.8734	0.133
39DAP/reference	0.82783	0.02
41DAP/reference	0.86184	0.096
42DAP/reference	0.82364	0.087
43DAP/reference	0.72656	0.02
47DAP/reference	0.97522	0.525
52DAP/reference	0.90927	0.268
57DAP/reference	0.78025	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21845	0.878
26DAP/20DAP	0.95835	1
34DAP/26DAP	1.01516
51DAP/34DAP	1.00737	1
52DAP/51DAP	0.87942	1
53DAP/52DAP	0.84857	0.089
55DAP/53DAP	0.88548	0.085
57DAP/55DAP	0.94037	0.694
62DAP/57DAP	0.99734	1
68DAP/62DAP	0.59088	0.227
68DAP/14DAP	0.52705	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.165	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.14811	0.752
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33327
Mature Eggplant/Ripe Tomato	0.24688	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8802	0.944
1-1-2/M82	1.00572
12-2/M82	N/A	N/A
12-4/M82	1.47035	1
1-3/M82	0.68604
2-1-1/M82	1.01438
2-1/M82	N/A	N/A
2-6/M82	1.07211	0.329
3-2/M82	0.84968
4-1-1/M82	1.01562	1
4-1/M82	1.17423
4-3-2/M82	0.72586	0.487
4-3/M82	N/A	N/A
5-3/M82	0.87681	0.642
6-2/M82	N/A	N/A
6-3/M82	1.19944	1
7-1/M82	1.02894
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08183	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.24803
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.67754
WT/WTpooled	0.83641

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	0.95724	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.21834	1
DC3000/delta hrp 24h	1.06609	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	0.97062	1
Var 0h	0.48364	0.291
Var 12h I row2-row1	1.00013	1
Var 12h NI row2-row1	0.80085	0.443
Var 36h I row2-row1	0.91484	1
Var 36h NI row2-row1	0.8476	0.45
Var 60h I row2-row1	1.379	0.562
Var 60h NI row2-row1	1.25689	0.904
Time course 0hI-0hNI	1.198	0.662
Time course 12hI-12hNI	0.94465	0.739
Time course 36hI-36hNI	0.84865	0.171
Time course 60hI-60hNI	1.13729	0.08

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00003	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82631	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.68803	0.333
Manapal/WT (red)	1.31147	0.164