Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62555	0.043
27DAP/17DAP	0.99747	1
39DAP/27DAP	0.98185	0.749
41DAP/39DAP	1.15082	0.494
42DAP/41DAP	0.77848	0.774
43DAP/42DAP	1.04361	1
47DAP/43DAP	1.02293	0.895
52DAP/47DAP	1.3247	0.624
57DAP/52DAP	0.72319	0.765

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8566	0.051
17DAP/reference	0.51591	0.006
27DAP/reference	0.55421	0.035
39DAP/reference	0.47882
41DAP/reference	N/A	N/A
42DAP/reference	0.87154	0.012
43DAP/reference	N/A	N/A
47DAP/reference	0.9751	0.503
52DAP/reference	0.41637	0.012
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78929	0.066
27DAP/17DAP	1.08963	0.754
39DAP/27DAP	0.68243	0.032
41DAP/39DAP	0.79357	0.164
42DAP/41DAP	0.89671	0.374
43DAP/42DAP	0.75815	0.028
47DAP/43DAP	0.88983	0.457
52DAP/47DAP	1.07998	0.844
57DAP/52DAP	0.91438	0.591
57DAP/7DAP	0.34385	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89929	0.138
17DAP/reference	1.14322	0.064
27DAP/reference	0.95558	0.325
39DAP/reference	0.99137	0.552
41DAP/reference	0.77477	0.021
42DAP/reference	0.98855	0.612
43DAP/reference	0.9606	0.421
47DAP/reference	0.98377	0.671
52DAP/reference	0.97834	0.523
57DAP/reference	0.98446	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67434	0.053
17DAP/reference	0.76218	0.092
27DAP/reference	0.76355	0.167
39DAP/reference	0.61625	0.007
41DAP/reference	0.75272	0.036
42DAP/reference	1.00672	0.723
43DAP/reference	0.87257	0.269
47DAP/reference	0.85878	0.056
52DAP/reference	0.64399	0.006
57DAP/reference	0.586	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07934	0.505
17DAP/reference	1.31445	0.376
27DAP/reference	1.11763	0.392
39DAP/reference	0.79288	0.083
41DAP/reference	0.98037	0.682
42DAP/reference	0.9452	0.445
43DAP/reference	0.98579	0.685
47DAP/reference	0.77735	0.036
52DAP/reference	0.81329	0.163
57DAP/reference	0.95817	0.402

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01415	1
26DAP/20DAP	0.97613	1
34DAP/26DAP	1.56179	0.077
51DAP/34DAP	0.701	0.174
52DAP/51DAP	1.03771	1
53DAP/52DAP	0.81509	0.358
55DAP/53DAP	0.90474	0.592
57DAP/55DAP	1.1643	0.745
62DAP/57DAP	0.84264	0.466
68DAP/62DAP	0.87945	0.668
68DAP/14DAP	0.77668	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81017	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53512	0.058
Mature Green Tomato/Ripe Tomato	2.9494	0.053
Immature Eggplant/Mature Eggplant	0.68235	0.063
Ripe Pepper/Ripe Tomato	1.1431	1
Mature Eggplant/Ripe Tomato	4.5825	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31756	0.591
1-1-2/M82	1.00352	1
12-2/M82	1.51434
12-4/M82	0.98506	1
1-3/M82	0.62469
2-1-1/M82	0.57961
2-1/M82	N/A	N/A
2-6/M82	0.7462	0.501
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.58057
4-3-2/M82	1.0306	0.262
4-3/M82	0.89552
5-3/M82	0.956	1
6-2/M82	N/A	N/A
6-3/M82	0.84175	1
7-1/M82	0.99583
7-2/M82	0.78751	0.599
9-3-2/M82	0.60727	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	0.61556
IL12-4/WTpooled	1.32931
IL1-4/WTpooled	1.20419	1
WT/WTpooled	0.9252	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	1.19748	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93373	1
DC3000/delta hrp 6h	1.09786	1
DC3000/delta hrp 12h	1.01195	1
DC3000/delta hrp 24h	0.56044	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44733	0.023
DC3000 delta B/DC3000 delta AB	0.42005	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03509	1
Exp 36h	0.84481	0.539
Exp 60h	0.99874	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99838	1
Var 0h	0.96235	1
Var 12h I row2-row1	0.93865	0.77
Var 12h NI row2-row1	1.19039	0.34
Var 36h I row2-row1	1.31047	0.305
Var 36h NI row2-row1	0.65559	0.432
Var 60h I row2-row1	1.48887	0.562
Var 60h NI row2-row1	0.67585	0.63
Time course 0hI-0hNI	0.96216	0.817
Time course 12hI-12hNI	0.99691	0.972
Time course 36hI-36hNI	1.58388	0.005
Time course 60hI-60hNI	1.53189	0.575

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)	0.96391	0.362
transgenic ySAMdc/azygous control (breaker)	0.8677	0.142
transgenic ySAMdc/azygous control (red)	1.03803	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85656	0.172

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.54	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.13071	0.084
Manapal/WT (break)	1.78771	0.183
Manapal/WT (red)	1.92325	0.164