Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.13.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77613	0.097
27DAP/17DAP	0.83129	0.606
39DAP/27DAP	0.78393	0.327
41DAP/39DAP	1.32593	0.413
42DAP/41DAP	1.03755	1
43DAP/42DAP	0.93416	0.877
47DAP/43DAP	0.96077	0.828
52DAP/47DAP	1.3725	0.545
57DAP/52DAP	1.06478	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02064	0.96
17DAP/reference	0.84378	0.01
27DAP/reference	0.89877	0.047
39DAP/reference	0.95716	0.565
41DAP/reference	0.88948	0.018
42DAP/reference	0.96554	0.12
43DAP/reference	0.92742	0.148
47DAP/reference	0.9538	0.065
52DAP/reference	1.0059	0.791
57DAP/reference	1.06333	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06363	0.482
27DAP/17DAP	0.98771	0.919
39DAP/27DAP	1.00029	1
41DAP/39DAP	1.00265	1
42DAP/41DAP	0.97221	0.715
43DAP/42DAP	0.97326	0.415
47DAP/43DAP	1.00595	0.951
52DAP/47DAP	0.98313	0.917
57DAP/52DAP	1.03643	0.763
57DAP/7DAP	1.00654	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91029	0.072
17DAP/reference	0.94808	0.028
27DAP/reference	1.01875	0.804
39DAP/reference	1.00749	0.705
41DAP/reference	1.0026	0.811
42DAP/reference	1.10007	0.013
43DAP/reference	1.01914	0.386
47DAP/reference	0.7994	0.222
52DAP/reference	0.99975	0.802
57DAP/reference	1.02237	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99325	0.869
17DAP/reference	0.92159	0.176
27DAP/reference	1.05765	1
39DAP/reference	0.78993	0.043
41DAP/reference	0.80604	0.048
42DAP/reference	0.97288	0.433
43DAP/reference	0.76543	0.034
47DAP/reference	0.98445	0.338
52DAP/reference	0.76977	0.004
57DAP/reference	0.79428	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09624	0.126
17DAP/reference	0.91428	0.189
27DAP/reference	0.973	0.539
39DAP/reference	1.01105	1
41DAP/reference	0.94837	0.512
42DAP/reference	0.87528	0.172
43DAP/reference	0.97479	0.568
47DAP/reference	0.76195	0.006
52DAP/reference	0.91843	0.455
57DAP/reference	0.81642	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00798	0.966
26DAP/20DAP	0.94713	0.512
34DAP/26DAP	0.96063	0.771
51DAP/34DAP	1.02354	0.829
52DAP/51DAP	0.98518	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.95375	0.784
57DAP/55DAP	0.91067	0.744
62DAP/57DAP	0.97225	0.871
68DAP/62DAP	1.02518	0.991
68DAP/14DAP	1.05273	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03841	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98684
Mature Green Tomato/Ripe Tomato	1.83112	0.03
Immature Eggplant/Mature Eggplant	2.27009	0.054
Ripe Pepper/Ripe Tomato	1.92311
Mature Eggplant/Ripe Tomato	8.5825

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91273	0.69
1-1-2/M82	0.89385	1
12-2/M82	0.9432	0.727
12-4/M82	0.86725	1
1-3/M82	1.04158	0.277
2-1-1/M82	1.09691	1
2-1/M82	N/A	N/A
2-6/M82	0.9403	0.501
3-2/M82	1.0825
4-1-1/M82	0.96796	1
4-1/M82	0.74524	0.867
4-3-2/M82	1.03948
4-3/M82	0.96558	1
5-3/M82	1.00336	1
6-2/M82	1.02375	1
6-3/M82	1.0002	1
7-1/M82	0.93986	1
7-2/M82	0.91831	0.565
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94471	1
IL2-6/WTpooled	1.0253	1
IL7-5/WTpooled	1.07246	0.792
IL7-3/WTpooled	1.03857	1
IL12-4/WTpooled	1.17751	0.52
IL1-4/WTpooled	1.03309	1
WT/WTpooled	0.95623	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	0.637	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95608	1
DC3000/delta hrp 6h	1.23153	1
DC3000/delta hrp 12h	0.94718	1
DC3000/delta hrp 24h	1.09322	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04358	0.515
DC3000 delta B/DC3000 delta AB	1.15403	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.7688	0.82
Exp 60h	0.35247	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99841	1
Var 0h	1.6481	0.98
Var 12h I row2-row1	1.15372	0.242
Var 12h NI row2-row1	1.01659	1
Var 36h I row2-row1	1.04236	1
Var 36h NI row2-row1	0.94416	0.706
Var 60h I row2-row1	1.13408	1
Var 60h NI row2-row1	1.02385	1
Time course 0hI-0hNI	1.04536	0.852
Time course 12hI-12hNI	1.00963	1
Time course 36hI-36hNI	1.00532	1
Time course 60hI-60hNI	1.2635	0.096

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)	0.85278	0.362
transgenic ySAMdc/azygous control (breaker)	1.37892	0.248
transgenic ySAMdc/azygous control (red)	1.37016	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98875	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23666	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.16858	0.087
Manapal/WT (break)	1.08087	1
Manapal/WT (red)	0.98073	0.863