Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.3.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99638	0.911
27DAP/17DAP	1.10024	0.881
39DAP/27DAP	0.89344	0.414
41DAP/39DAP	1.46489	0.084
42DAP/41DAP	1.01776	1
43DAP/42DAP	1.01151	0.937
47DAP/43DAP	1.54585	0.555
52DAP/47DAP	1.23308	0.757
57DAP/52DAP	0.90447	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06773	0.278
17DAP/reference	0.98253	0.701
27DAP/reference	0.89277	0.444
39DAP/reference	0.94845	0.734
41DAP/reference	1.00469	1
42DAP/reference	1.29274	0.005
43DAP/reference	0.9617	0.785
47DAP/reference	1.4609	0.009
52DAP/reference	0.97624	0.564
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04719	0.881
27DAP/17DAP	1.03937	0.957
39DAP/27DAP	1.08769	0.707
41DAP/39DAP	0.86676	0.53
42DAP/41DAP	1.17471	0.378
43DAP/42DAP	1.08575	0.478
47DAP/43DAP	0.95659	0.787
52DAP/47DAP	1.06554	0.789
57DAP/52DAP	0.86237	0.221
57DAP/7DAP	0.86603	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77785	0.046
17DAP/reference	3.66261	0.008
27DAP/reference	2.5066	0.006
39DAP/reference	2.76253	0.005
41DAP/reference	3.00266	0.011
42DAP/reference	3.0966	0.006
43DAP/reference	4.92352	0.006
47DAP/reference	2.48741	0.187
52DAP/reference	3.40474	0.007
57DAP/reference	3.16394	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06422	0.823
17DAP/reference	1.03703	0.789
27DAP/reference	1.11278	0.244
39DAP/reference	0.9281	0.159
41DAP/reference	0.91052	0.177
42DAP/reference	0.94036	0.237
43DAP/reference	0.87594	0.277
47DAP/reference	1.02442	1
52DAP/reference	0.93005	0.22
57DAP/reference	1.02722	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.79811	0.037
17DAP/reference	1.3525	0.394
27DAP/reference	3.07218	0.017
39DAP/reference	2.66805	0.01
41DAP/reference	2.2128	0.01
42DAP/reference	2.66839	0.008
43DAP/reference	2.29704	0.021
47DAP/reference	1.65644	0.006
52DAP/reference	3.01765	0.036
57DAP/reference	2.06689	0.094

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03144	1
26DAP/20DAP	0.80583	0.244
34DAP/26DAP	0.9355	0.841
51DAP/34DAP	1.08329	0.565
52DAP/51DAP	1.05227	0.722
53DAP/52DAP	1.15763	0.134
55DAP/53DAP	1.26198	0.236
57DAP/55DAP	1.08301	0.947
62DAP/57DAP	0.29194	0.002
68DAP/62DAP	1.29752	0.247
68DAP/14DAP	1.20797	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19559	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40003	0.058
Mature Green Tomato/Ripe Tomato	1.8639	0.064
Immature Eggplant/Mature Eggplant	0.53619	0.057
Ripe Pepper/Ripe Tomato	0.38415	0.224
Mature Eggplant/Ripe Tomato	0.51502	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04187	1
1-1-2/M82	1.28133	1
12-2/M82	0.94045	0.955
12-4/M82	1.09904	1
1-3/M82	1.86382	0.248
2-1-1/M82	0.95604	1
2-1/M82	0.50443	0.345
2-6/M82	0.8859	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.92916	1
4-1/M82	1.15904
4-3-2/M82	1.686
4-3/M82	1.22694	1
5-3/M82	0.83098	1
6-2/M82	0.89674	1
6-3/M82	1.06658	1
7-1/M82	0.87315	0.408
7-2/M82	0.74394	0.42
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90195	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.93173	1
IL1-4/WTpooled	1.00978	1
WT/WTpooled	0.87615

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	1.07369	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0215	0.894
DC3000/delta hrp 6h	0.98294	0.95
DC3000/delta hrp 12h	1.10648	1
DC3000/delta hrp 24h	0.56041	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44314
DC3000 delta B/DC3000 delta AB	0.87576	0.307

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97101	1
Exp 36h	0.82513	0.449
Exp 60h	0.71915	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.89908	0.289
transgenic ySAMdc/azygous control (breaker)	0.78044	0.173
transgenic ySAMdc/azygous control (red)	0.77573	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98756	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58059	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.52853	0.09
Manapal/WT (break)	1.70309	0.381
Manapal/WT (red)	0.96489	0.728