Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81158	0.148
27DAP/17DAP	0.64658	0.069
39DAP/27DAP	1.18571	0.667
41DAP/39DAP	2.23009	0.25
42DAP/41DAP	1.71177	0.041
43DAP/42DAP	1.53985	0.44
47DAP/43DAP	0.4793	0.049
52DAP/47DAP	0.91188	0.702
57DAP/52DAP	1.16494	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83563	0.132
17DAP/reference	0.69535	0.091
27DAP/reference	0.76225	0.095
39DAP/reference	0.82573	0.076
41DAP/reference	0.67572	0.009
42DAP/reference	1.01435	1
43DAP/reference	0.65827	0.047
47DAP/reference	0.75218	0.003
52DAP/reference	0.88308	0.177
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8716	0.126
27DAP/17DAP	0.90499	0.684
39DAP/27DAP	1.13599	0.587
41DAP/39DAP	0.69097	0.022
42DAP/41DAP	1.4937	0.006
43DAP/42DAP	2.573	0.014
47DAP/43DAP	0.69126	0.009
52DAP/47DAP	1.1356	0.593
57DAP/52DAP	0.76494	0.067
57DAP/7DAP	0.96794	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32374	0.035
17DAP/reference	0.97775	0.447
27DAP/reference	0.86861	0.055
39DAP/reference	1.18215	0.114
41DAP/reference	0.97372	0.489
42DAP/reference	1.03117	1
43DAP/reference	1.43437	0.056
47DAP/reference	1.21237	0.084
52DAP/reference	0.92619	0.304
57DAP/reference	0.84094	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83077	0.19
17DAP/reference	0.84121	0.068
27DAP/reference	0.88864	0.111
39DAP/reference	0.93069	0.322
41DAP/reference	1.0259	0.862
42DAP/reference	1.3622	0.621
43DAP/reference	0.8606	0.307
47DAP/reference	0.99221	0.643
52DAP/reference	0.77615	0.006
57DAP/reference	0.61121	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19934	0.224
17DAP/reference	1.06901	0.558
27DAP/reference	0.99092	0.691
39DAP/reference	0.97191	0.504
41DAP/reference	0.9923	0.754
42DAP/reference	1.54025	0.03
43DAP/reference	1.90341	0.007
47DAP/reference	1.14432	0.133
52DAP/reference	1.20746	0.324
57DAP/reference	1.11883	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97303	1
26DAP/20DAP	0.84065	0.512
34DAP/26DAP	1.55473	1
51DAP/34DAP	1.03246	0.957
52DAP/51DAP	1.02953	1
53DAP/52DAP	1.06291	1
55DAP/53DAP	1.34507	0.184
57DAP/55DAP	0.92055	0.694
62DAP/57DAP	0.98216	1
68DAP/62DAP	1.53188	0.21
68DAP/14DAP	1.26056	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.40012	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.53138	0.11
Mature Green Tomato/Ripe Tomato	1.37541	0.399
Immature Eggplant/Mature Eggplant	0.64065	0.063
Ripe Pepper/Ripe Tomato	2.39636	0.256
Mature Eggplant/Ripe Tomato	0.71722	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.83888	0.526
1-1-2/M82	1.03481
12-2/M82	0.8803	0.955
12-4/M82	0.73019	1
1-3/M82	1.77054	0.479
2-1-1/M82	0.66508	0.683
2-1/M82	0.5838	0.519
2-6/M82	1.61847	0.594
3-2/M82	1.7112
4-1-1/M82	1.30134	1
4-1/M82	0.95833
4-3-2/M82	2.43606
4-3/M82	2.37179	0.268
5-3/M82	0.89656	1
6-2/M82	2.15078	0.253
6-3/M82	0.98831	1
7-1/M82	0.81109	0.509
7-2/M82	1.90616	0.385
9-3-2/M82	1.8252	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72063	0.321
IL2-6/WTpooled	0.75388
IL7-5/WTpooled	1.10845
IL7-3/WTpooled	0.6488
IL12-4/WTpooled	0.9022	0.71
IL1-4/WTpooled	1.09783	1
WT/WTpooled	0.94877	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	0.94336	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91802	1
DC3000/delta hrp 6h	0.91282	0.95
DC3000/delta hrp 12h	0.93628	1
DC3000/delta hrp 24h	0.85195	0.098

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78412	0.232
DC3000 delta B/DC3000 delta AB	0.78431	0.036

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97361	1
Exp 36h	0.68288	0.406
Exp 60h	0.75003	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06746	1
Var 0h	0.8223	0.933
Var 12h I row2-row1	1.16433	0.613
Var 12h NI row2-row1	1.06717	1
Var 36h I row2-row1	1.12798	0.601
Var 36h NI row2-row1	1.08889	1
Var 60h I row2-row1	0.9804	1
Var 60h NI row2-row1	0.88983	0.329
Time course 0hI-0hNI	1.07493	0.833
Time course 12hI-12hNI	1.00044	1
Time course 36hI-36hNI	1.29856	0.008
Time course 60hI-60hNI	1.75993	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)	0.96943	0.614
transgenic ySAMdc/azygous control (breaker)	2.46925	0.162
transgenic ySAMdc/azygous control (red)	1.39291	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02014	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13719	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.04492	0.14
Manapal/WT (break)	1.34631	1
Manapal/WT (red)	2.23495	0.137