Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34173	0.394
27DAP/17DAP	1.45079	0.801
39DAP/27DAP	1.18753	0.713
41DAP/39DAP	1.34833	0.54
42DAP/41DAP	1.39968	0.488
43DAP/42DAP	0.99399	0.937
47DAP/43DAP	0.64679	0.088
52DAP/47DAP	1.33925	0.597
57DAP/52DAP	0.83794	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01267	0.846
17DAP/reference	0.97712	0.536
27DAP/reference	0.99712	0.867
39DAP/reference	0.99259	0.874
41DAP/reference	0.92515	0.085
42DAP/reference	1.0013	0.731
43DAP/reference	0.97265	0.538
47DAP/reference	0.96968	0.161
52DAP/reference	0.96385	0.405
57DAP/reference	1.07563	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16051	0.119
27DAP/17DAP	1.01948	0.976
39DAP/27DAP	0.78442	0.034
41DAP/39DAP	1.25886	0.469
42DAP/41DAP	1.24335	0.301
43DAP/42DAP	1.91013	0.013
47DAP/43DAP	1.03663	0.926
52DAP/47DAP	2.36029	0.036
57DAP/52DAP	3.11163	0.069
57DAP/7DAP	5.64697	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87669	0.031
17DAP/reference	1.55072	0.007
27DAP/reference	1.10597	0.301
39DAP/reference	1.55141	0.011
41DAP/reference	1.22748	0.075
42DAP/reference	1.42786	0.405
43DAP/reference	1.50473	0.012
47DAP/reference	1.17403	0.571
52DAP/reference	1.75522	0.007
57DAP/reference	1.58363	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01208	0.812
17DAP/reference	0.9702	0.434
27DAP/reference	1.04206	0.67
39DAP/reference	0.97793	0.322
41DAP/reference	0.92994	0.127
42DAP/reference	0.9509	0.15
43DAP/reference	1.04166	0.777
47DAP/reference	0.93643	0.168
52DAP/reference	0.99373	0.619
57DAP/reference	1.04454	0.423

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37125	0.031
17DAP/reference	1.21922	0.412
27DAP/reference	1.29169	0.067
39DAP/reference	1.23168	0.027
41DAP/reference	1.32124	0.028
42DAP/reference	1.17745	0.226
43DAP/reference	1.12307	0.505
47DAP/reference	0.84792	0.021
52DAP/reference	1.35956	0.278
57DAP/reference	0.86575	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00153	1
26DAP/20DAP	1.13115	1
34DAP/26DAP	0.39885	0.076
51DAP/34DAP	0.91676	0.703
52DAP/51DAP	1.041	0.704
53DAP/52DAP	1.0001	0.998
55DAP/53DAP	1.10404	0.798
57DAP/55DAP	1.25151	0.881
62DAP/57DAP	1.53848	0.622
68DAP/62DAP	0.745	0.579
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.59264	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.31749	0.058
Mature Green Tomato/Ripe Tomato	0.4004	0.017
Immature Eggplant/Mature Eggplant	1.18553	0.07
Ripe Pepper/Ripe Tomato	0.73834	1
Mature Eggplant/Ripe Tomato	1.01258	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30524	0.505
1-1-2/M82	1.17338	0.977
12-2/M82	2.38425	1
12-4/M82	0.99346	1
1-3/M82	1.52814
2-1-1/M82	0.73487
2-1/M82	0.92497	0.519
2-6/M82	0.86591	1
3-2/M82	2.15753
4-1-1/M82	0.85228	1
4-1/M82	1.36174	0.853
4-3-2/M82	1.23028	1
4-3/M82	1.09185	0.268
5-3/M82	0.66813	0.49
6-2/M82	2.56863	0.253
6-3/M82	0.97987
7-1/M82	0.96362
7-2/M82	0.95044
9-3-2/M82	0.96546	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95388	1
IL2-6/WTpooled	1.00378	1
IL7-5/WTpooled	0.75262	1
IL7-3/WTpooled	1.10948	1
IL12-4/WTpooled	0.83102	0.478
IL1-4/WTpooled	1.02525	1
WT/WTpooled	0.85066	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	1.0888	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.22373
DC3000/delta hrp 6h	1.10288	0.95
DC3000/delta hrp 12h	0.97632	1
DC3000/delta hrp 24h	0.86188	0.274

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11986	0.208
DC3000 delta B/DC3000 delta AB	1.25172	0.249

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02367	1
Exp 36h	0.92146	0.879
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02286	1
Var 0h	0.99633	1
Var 12h I row2-row1	1.89549	0.473
Var 12h NI row2-row1	1.17592	0.649
Var 36h I row2-row1	0.74229	0.438
Var 36h NI row2-row1	1.48154	1
Var 60h I row2-row1	0.57245	0.285
Var 60h NI row2-row1	1.40671	0.904
Time course 0hI-0hNI	1.13574	0.63
Time course 12hI-12hNI	0.9147	0.442
Time course 36hI-36hNI	0.92212	0.25
Time course 60hI-60hNI	4.5954	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)	0.91036	0.428
transgenic ySAMdc/azygous control (breaker)	1.17538	0.248
transgenic ySAMdc/azygous control (red)	1.2405	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00613	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81345	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96962	1
Manapal/WT (break)	1.17334	1
Manapal/WT (red)	1.026	1