Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36975	0.142
27DAP/17DAP	0.92437	0.846
39DAP/27DAP	0.95806	0.652
41DAP/39DAP	1.20706	0.282
42DAP/41DAP	1.18159	0.82
43DAP/42DAP	0.98783	0.937
47DAP/43DAP	1.42714	0.455
52DAP/47DAP	1.11491	0.976
57DAP/52DAP	1.10073	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84535	0.075
17DAP/reference	1.11127	0.306
27DAP/reference	1.19347	0.111
39DAP/reference	1.2233	0.413
41DAP/reference	1.21074	0.062
42DAP/reference	1.23681	0.001
43DAP/reference	1.48533	0.007
47DAP/reference	1.96774	0.001
52DAP/reference	1.87786	0.007
57DAP/reference	1.6346	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34103	0.04
27DAP/17DAP	0.88878	0.195
39DAP/27DAP	1.04396	0.575
41DAP/39DAP	1.00114	1
42DAP/41DAP	0.93523	0.379
43DAP/42DAP	1.0909	0.273
47DAP/43DAP	1.05836	0.735
52DAP/47DAP	1.15838	0.449
57DAP/52DAP	1.00264	0.926
57DAP/7DAP	1.12983	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18131	0.124
17DAP/reference	1.32853	0.007
27DAP/reference	1.28827	0.008
39DAP/reference	1.30949	0.011
41DAP/reference	1.26341	0.028
42DAP/reference	1.0869	0.686
43DAP/reference	1.14924	0.273
47DAP/reference	1.25672	0.033
52DAP/reference	1.20517	0.197
57DAP/reference	1.26901	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8616	0.038
17DAP/reference	1.26955	0.089
27DAP/reference	1.10548	0.338
39DAP/reference	1.27178	0.018
41DAP/reference	1.20015	0.086
42DAP/reference	1.26887	0.021
43DAP/reference	1.1367	0.396
47DAP/reference	1.54452	0.008
52DAP/reference	1.10947	0.417
57DAP/reference	1.14355	0.609

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	6.29139	0.018
17DAP/reference	1.19102	0.538
27DAP/reference	2.70328	0.039
39DAP/reference	1.19211	0.104
41DAP/reference	1.28484	0.096
42DAP/reference	6.39105	0.022
43DAP/reference	5.14092	0.013
47DAP/reference	1.99278	0.006
52DAP/reference	7.4814	0.031
57DAP/reference	4.19071	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99679	1
26DAP/20DAP	0.97972	1
34DAP/26DAP	1.04941	1
51DAP/34DAP	1.03723	0.854
52DAP/51DAP	0.95338	1
53DAP/52DAP	1.01587	0.944
55DAP/53DAP	0.93572	0.417
57DAP/55DAP	0.94394	0.715
62DAP/57DAP	1.03669	1
68DAP/62DAP	1.14993	0.713
68DAP/14DAP	0.69442	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.62886	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06833	0.417
Mature Green Tomato/Ripe Tomato	0.59647	0.02
Immature Eggplant/Mature Eggplant	1.01701	0.633
Ripe Pepper/Ripe Tomato	0.26297	0.224
Mature Eggplant/Ripe Tomato	0.22348	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22895	0.742
1-1-2/M82	0.75442	0.977
12-2/M82	0.78512	0.862
12-4/M82	1.15411	1
1-3/M82	1.36953	0.479
2-1-1/M82	0.89604	0.784
2-1/M82	0.81759	0.322
2-6/M82	1.09693	1
3-2/M82	0.77687
4-1-1/M82	0.62341
4-1/M82	1.22059	1
4-3-2/M82	1.00497	1
4-3/M82	1.24592	1
5-3/M82	0.89493	1
6-2/M82	N/A	N/A
6-3/M82	1.0637	1
7-1/M82	N/A	N/A
7-2/M82	0.94125	0.599
9-3-2/M82	1.24492	0.182

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	0.88916
IL12-4/WTpooled	0.62943
IL1-4/WTpooled	1.49488	1
WT/WTpooled	1.18834

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	0.98056	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03385	0.75
DC3000/delta hrp 6h	1.09226	1
DC3000/delta hrp 12h	1.31952	1
DC3000/delta hrp 24h	0.61153	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31129	0.598
DC3000 delta B/DC3000 delta AB	0.94885	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02145	1
Exp 36h	0.70864	0.456
Exp 60h	0.78718	0.454

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	0.94585	0.457
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)	1.09831	0.455
transgenic ySAMdc/azygous control (breaker)	0.6411	0.131
transgenic ySAMdc/azygous control (red)	0.9916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13585	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55407	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64529	0.172
Manapal/WT (break)	1.25088	0.381
Manapal/WT (red)	1.00689	1