Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02904	0.977
27DAP/17DAP	1.13385	0.845
39DAP/27DAP	1.41229	0.191
41DAP/39DAP	1.10101	0.649
42DAP/41DAP	0.91355	0.774
43DAP/42DAP	0.94595	0.867
47DAP/43DAP	1.07601	0.793
52DAP/47DAP	1.15858	0.646
57DAP/52DAP	0.98332	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96401	0.422
17DAP/reference	0.96432	0.321
27DAP/reference	0.97436	0.369
39DAP/reference	0.99122	0.841
41DAP/reference	0.90905	0.267
42DAP/reference	0.96384	0.151
43DAP/reference	0.99686	0.904
47DAP/reference	0.92332	0.065
52DAP/reference	0.89609	0.223
57DAP/reference	0.91026	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88521	0.277
27DAP/17DAP	0.90665	0.446
39DAP/27DAP	1.0795	0.378
41DAP/39DAP	1.01774	0.921
42DAP/41DAP	0.98498	0.809
43DAP/42DAP	1.05659	0.23
47DAP/43DAP	1.07867	0.339
52DAP/47DAP	0.98834	0.935
57DAP/52DAP	0.9676	0.678
57DAP/7DAP	1.07761	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90399
17DAP/reference	1.0284	1
27DAP/reference	0.92209	0.037
39DAP/reference	0.85969	0.011
41DAP/reference	0.89402	0.06
42DAP/reference	0.86044	0.022
43DAP/reference	0.8718	0.015
47DAP/reference	1.00285	1
52DAP/reference	0.81395	0.023
57DAP/reference	0.87125	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94575	0.441
17DAP/reference	0.89549	0.059
27DAP/reference	0.88409	0.111
39DAP/reference	0.80329	0.012
41DAP/reference	0.95264	0.098
42DAP/reference	0.86639	0.039
43DAP/reference	0.97231	0.581
47DAP/reference	0.9998	0.812
52DAP/reference	0.89303	0.02
57DAP/reference	0.81407	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85647	0.071
17DAP/reference	0.89751	0.106
27DAP/reference	1.00008	0.883
39DAP/reference	0.93046	0.101
41DAP/reference	1.02589	0.777
42DAP/reference	1.05244	0.443
43DAP/reference	0.93127	0.197
47DAP/reference	1.09293	0.081
52DAP/reference	0.95093	0.551
57DAP/reference	0.83137	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96558	1
26DAP/20DAP	1.13578	0.487
34DAP/26DAP	1.10199	0.542
51DAP/34DAP	0.91765	0.498
52DAP/51DAP	1.03947	0.783
53DAP/52DAP	1.01013	0.961
55DAP/53DAP	1.02849	0.834
57DAP/55DAP	1.05636	0.694
62DAP/57DAP	1.05626	0.622
68DAP/62DAP	1.04451	0.945
68DAP/14DAP	0.93004	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14309	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.31882	0.11
Mature Green Tomato/Ripe Tomato	1.38126	0.02
Immature Eggplant/Mature Eggplant	1.42366	0.085
Ripe Pepper/Ripe Tomato	0.54466	0.293
Mature Eggplant/Ripe Tomato	0.22288	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95769	0.944
1-1-2/M82	0.97645	1
12-2/M82	0.99451	1
12-4/M82	1.0032	1
1-3/M82	1.23564	0.479
2-1-1/M82	1.03123
2-1/M82	0.85706
2-6/M82	1.18018
3-2/M82	1.09194	0.84
4-1-1/M82	0.84912	1
4-1/M82	1.07253	1
4-3-2/M82	0.98036	1
4-3/M82	0.9773	1
5-3/M82	0.96924	1
6-2/M82	1.23308
6-3/M82	N/A	N/A
7-1/M82	1.18568	1
7-2/M82	1.17681	0.385
9-3-2/M82	0.91103	0.449

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.04308	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94507	1
DC3000/delta hrp 6h	0.99643	0.95
DC3000/delta hrp 12h	1.2012	1
DC3000/delta hrp 24h	0.96931	0.808

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06856	0.408
DC3000 delta B/DC3000 delta AB	1.01025	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11084	0.254
Exp 36h	0.81079	0.449
Exp 60h	0.89547	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98975	1
Var 0h	1.37477	0.98
Var 12h I row2-row1	1.09067	0.379
Var 12h NI row2-row1	0.92264	0.546
Var 36h I row2-row1	1.12033	1
Var 36h NI row2-row1	1.03291	1
Var 60h I row2-row1	0.9382	0.582
Var 60h NI row2-row1	0.99561	1
Time course 0hI-0hNI	1.02535	0.63
Time course 12hI-12hNI	1.04293	0.567
Time course 36hI-36hNI	1.09078	0.028
Time course 60hI-60hNI	1.17453	0.008

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)	0.99299	0.862
transgenic ySAMdc/azygous control (breaker)	0.52425	0.131
transgenic ySAMdc/azygous control (red)	1.1047	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95144	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60892	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10719	1
Manapal/WT (break)	0.93901	1
Manapal/WT (red)	1.0004	1