Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.12.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94396	0.689
27DAP/17DAP	1.1239	0.849
39DAP/27DAP	0.92485	0.549
41DAP/39DAP	1.1932	0.494
42DAP/41DAP	0.81377	0.774
43DAP/42DAP	1.05708	1
47DAP/43DAP	0.86099	0.562
52DAP/47DAP	0.84863	0.607
57DAP/52DAP	0.99211	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.83086	0.007
17DAP/reference	0.96745	0.597
27DAP/reference	0.74462	0.035
39DAP/reference	0.92535	0.261
41DAP/reference	0.93825	0.434
42DAP/reference	0.91553	0.107
43DAP/reference	0.91231	0.36
47DAP/reference	0.83191	0.046
52DAP/reference	0.81263	0.105
57DAP/reference	0.75493	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70172	0.085
27DAP/17DAP	1.09343	0.887
39DAP/27DAP	0.68957	0.039
41DAP/39DAP	1.05269	1
42DAP/41DAP	1.13003	0.852
43DAP/42DAP	1.20254	0.212
47DAP/43DAP	0.83974	0.305
52DAP/47DAP	0.94218	0.839
57DAP/52DAP	1.84207	0.424
57DAP/7DAP	0.76541	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43471	0.037
17DAP/reference	1.14477	0.399
27DAP/reference	1.10487	0.453
39DAP/reference	0.91273	0.198
41DAP/reference	1.03103	0.848
42DAP/reference	1.10308	0.686
43DAP/reference	0.96529	0.403
47DAP/reference	0.92619	0.293
52DAP/reference	0.86211	0.097
57DAP/reference	0.90887	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50081	0.038
17DAP/reference	1.28654	0.21
27DAP/reference	1.32267	0.045
39DAP/reference	0.97423	0.526
41DAP/reference	1.15083	0.327
42DAP/reference	1.02443	1
43DAP/reference	1.19179	0.044
47DAP/reference	0.94222	0.137
52DAP/reference	0.80719	0.014
57DAP/reference	0.856	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45237	0.02
17DAP/reference	1.08116	0.558
27DAP/reference	1.06258	0.644
39DAP/reference	0.83562	0.028
41DAP/reference	0.93093	0.293
42DAP/reference	1.06972	0.877
43DAP/reference	1.0034	0.685
47DAP/reference	0.90454	0.249
52DAP/reference	0.7869	0.223
57DAP/reference	0.98495	0.623

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.91993	0.56
26DAP/20DAP	1.81239	0.112
34DAP/26DAP	0.88135	0.763
51DAP/34DAP	1.13772	0.936
52DAP/51DAP	0.81264	1
53DAP/52DAP	0.65249	0.078
55DAP/53DAP	1.00694	0.775
57DAP/55DAP	1.10116	0.865
62DAP/57DAP	0.99623	1
68DAP/62DAP	0.81006	0.505
68DAP/14DAP	0.85573	0.078

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11129	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86516	0.351
Mature Green Tomato/Ripe Tomato	1.70185	0.023
Immature Eggplant/Mature Eggplant	1.08891	0.23
Ripe Pepper/Ripe Tomato	1.34975	1
Mature Eggplant/Ripe Tomato	1.54193	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18085	0.742
1-1-2/M82	1.11576	1
12-2/M82	0.82588
12-4/M82	0.85393
1-3/M82	0.90775
2-1-1/M82	1.21463
2-1/M82	N/A	N/A
2-6/M82	1.16531	0.385
3-2/M82	N/A	N/A
4-1-1/M82	1.7694	0.735
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	2.21847	0.268
5-3/M82	1.03749	1
6-2/M82	1.14198	1
6-3/M82	1.04228	1
7-1/M82	0.93726
7-2/M82	1.42603	0.291
9-3-2/M82	1.5064

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05972
IL2-6/WTpooled	1.05897	1
IL7-5/WTpooled	0.92541
IL7-3/WTpooled	0.85867	0.31
IL12-4/WTpooled	0.69596	0.543
IL1-4/WTpooled	0.96318	1
WT/WTpooled	1.02078	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	1.39994	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96715	1
DC3000/delta hrp 6h	1.14665	1
DC3000/delta hrp 12h	1.18717	1
DC3000/delta hrp 24h	1.21431	0.37

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62713
DC3000 delta B/DC3000 delta AB	0.90246	0.575

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96412	1
Exp 36h	1.1035	1
Exp 60h	0.89996	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99296	1
Var 0h	0.50786	1
Var 12h I row2-row1	0.87423	0.338
Var 12h NI row2-row1	1.18737	0.235
Var 36h I row2-row1	0.96095	0.203
Var 36h NI row2-row1	0.85077	0.432
Var 60h I row2-row1	0.87217	0.832
Var 60h NI row2-row1	0.6824	0.904
Time course 0hI-0hNI	0.84698	0.16
Time course 12hI-12hNI	1.04405	0.774
Time course 36hI-36hNI	1.0295	0.798
Time course 60hI-60hNI	1.06084	0.359

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)	0.99879	1
transgenic ySAMdc/azygous control (breaker)	0.79776	0.15
transgenic ySAMdc/azygous control (red)	0.90031	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98453	0.534

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01995	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91583	1
Manapal/WT (break)	0.80048	1
Manapal/WT (red)	1.34859	0.413