Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8634	0.364
27DAP/17DAP	0.6146	0.053
39DAP/27DAP	0.71267	0.382
41DAP/39DAP	0.71351	0.123
42DAP/41DAP	0.79931	0.774
43DAP/42DAP	1.01718	0.937
47DAP/43DAP	0.89247	0.64
52DAP/47DAP	0.97016	0.842
57DAP/52DAP	1.11162	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35536	0.403
17DAP/reference	0.9539	0.567
27DAP/reference	0.86553	0.349
39DAP/reference	0.72344	0.039
41DAP/reference	0.92751	0.542
42DAP/reference	0.7741	0.038
43DAP/reference	0.73184
47DAP/reference	0.74971	0.025
52DAP/reference	0.65421	0.028
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78667	0.105
27DAP/17DAP	0.8634	0.339
39DAP/27DAP	0.511	0.028
41DAP/39DAP	1.23063	0.579
42DAP/41DAP	0.87168	0.282
43DAP/42DAP	0.81761	0.165
47DAP/43DAP	0.99641	0.933
52DAP/47DAP	1.00103	0.925
57DAP/52DAP	1.0794	0.745
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31901	0.046
17DAP/reference	0.90512	0.072
27DAP/reference	0.80951	0.01
39DAP/reference	0.75253	0.011
41DAP/reference	0.77215	0.015
42DAP/reference	0.72708	0.01
43DAP/reference	0.7337	0.014
47DAP/reference	0.7506	0.036
52DAP/reference	0.71884	0.011
57DAP/reference	0.70815	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33874	0.038
17DAP/reference	1.06999	0.599
27DAP/reference	0.90495	0.129
39DAP/reference	0.7417	0.007
41DAP/reference	0.79264	0.096
42DAP/reference	0.86792	0.073
43DAP/reference	0.84664	0.075
47DAP/reference	0.84274	0.085
52DAP/reference	0.70142	0.016
57DAP/reference	0.84647	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.80877	0.016
17DAP/reference	1.57254	0.091
27DAP/reference	1.00415	1
39DAP/reference	0.88202	0.083
41DAP/reference	0.86933	0.058
42DAP/reference	0.76559	0.016
43DAP/reference	0.68978	0.02
47DAP/reference	0.73149	0.015
52DAP/reference	0.9266	0.505
57DAP/reference	1.17337	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11299	0.966
26DAP/20DAP	0.66333	0.512
34DAP/26DAP	0.69664	0.194
51DAP/34DAP	1.03644	0.937
52DAP/51DAP	1.08765	0.939
53DAP/52DAP	0.89868	0.52
55DAP/53DAP	1.37267	0.218
57DAP/55DAP	1.04602	0.898
62DAP/57DAP	1.33393	0.024
68DAP/62DAP	0.78435	0.055
68DAP/14DAP	1.25329

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.47497	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.04607
Mature Green Tomato/Ripe Tomato	15.7235	0.015
Immature Eggplant/Mature Eggplant	0.23856	0.062
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	18.0706	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.15325	0.611
1-3/M82	0.6117	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.86525
4-1-1/M82	N/A	N/A
4-1/M82	1.65391
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.1684	0.572
6-2/M82	0.99235
6-3/M82	1.19448
7-1/M82	N/A	N/A
7-2/M82	1.103
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9528	1
IL2-6/WTpooled	1.14621	0.659
IL7-5/WTpooled	0.99244	1
IL7-3/WTpooled	1.17515	1
IL12-4/WTpooled	0.92142	1
IL1-4/WTpooled	0.93311	0.834
WT/WTpooled	0.98619	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	0.98345	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9832	1
DC3000/delta hrp 6h	1.24887	0.978
DC3000/delta hrp 12h	0.37126
DC3000/delta hrp 24h	0.86708	0.319

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4542	0.026
DC3000 delta B/DC3000 delta AB	0.35197	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92884	1
Exp 36h	0.61774	0.406
Exp 60h	0.69577	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9959	1
Var 0h	1.01042	1
Var 12h I row2-row1	0.92197	0.77
Var 12h NI row2-row1	0.89243	0.546
Var 36h I row2-row1	1.37223	0.41
Var 36h NI row2-row1	0.96982	0.791
Var 60h I row2-row1	0.79484	0.582
Var 60h NI row2-row1	1.1182	0.904
Time course 0hI-0hNI	1.06551	0.603
Time course 12hI-12hNI	1.03688	0.747
Time course 36hI-36hNI	0.99096	0.665
Time course 60hI-60hNI	1.93516	0.019

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)	0.96846	0.722
transgenic ySAMdc/azygous control (breaker)	1.78323	0.248
transgenic ySAMdc/azygous control (red)	1.3641	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75325	0.093

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.49737	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.90272	0.083
Manapal/WT (break)	5.65203	0.13
Manapal/WT (red)	2.37738	0.222