Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32126	0.272
27DAP/17DAP	0.91562	0.822
39DAP/27DAP	1.31922	0.533
41DAP/39DAP	0.6379	0.071
42DAP/41DAP	0.84733	1
43DAP/42DAP	0.9255	0.864
47DAP/43DAP	0.77511	0.326
52DAP/47DAP	1.15948	0.691
57DAP/52DAP	1.06009	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55794	0.013
17DAP/reference	1.05955	0.777
27DAP/reference	0.77184	0.03
39DAP/reference	0.8956	0.342
41DAP/reference	0.99666	0.814
42DAP/reference	0.85643	0.034
43DAP/reference	0.74263	0.043
47DAP/reference	0.71479	0.003
52DAP/reference	0.57825	0.022
57DAP/reference	0.87204	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22799	0.093
27DAP/17DAP	0.87672	0.475
39DAP/27DAP	0.74611	0.088
41DAP/39DAP	1.39855	0.682
42DAP/41DAP	0.92488	0.499
43DAP/42DAP	0.71065	0.023
47DAP/43DAP	1.1156	0.772
52DAP/47DAP	0.8721	0.304
57DAP/52DAP	0.98228	0.793
57DAP/7DAP	0.42193	0.149

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94914	0.024
17DAP/reference	1.4702	0.006
27DAP/reference	1.49569	0.006
39DAP/reference	1.64262	0.008
41DAP/reference	1.44566	0.011
42DAP/reference	1.50656	0.007
43DAP/reference	1.2929	0.008
47DAP/reference	1.05832	1
52DAP/reference	1.63844	0.011
57DAP/reference	1.42066	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12719	0.75
17DAP/reference	1.60947	0.026
27DAP/reference	1.30513	0.044
39DAP/reference	1.47223	0.015
41DAP/reference	0.99179	0.557
42DAP/reference	1.00833	1
43DAP/reference	1.12218	0.617
47DAP/reference	1.05398	0.841
52DAP/reference	1.24394	0.05
57DAP/reference	0.85843	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71308	0.015
17DAP/reference	1.24948	0.273
27DAP/reference	1.32646	0.049
39DAP/reference	1.40406	0.018
41DAP/reference	1.27483	0.022
42DAP/reference	1.18689	0.716
43DAP/reference	1.10995	0.254
47DAP/reference	0.51203	0.005
52DAP/reference	0.94939	0.538
57DAP/reference	1.0254	0.613

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.70144	1
26DAP/20DAP	1.46397	0.235
34DAP/26DAP	1.21498	0.819
51DAP/34DAP	1.01496	1
52DAP/51DAP	0.94724	1
53DAP/52DAP	0.87005	0.374
55DAP/53DAP	0.84308	0.195
57DAP/55DAP	1.19982	0.203
62DAP/57DAP	0.79854	0.05
68DAP/62DAP	1.33971	0.85
68DAP/14DAP	0.74433	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29397	0.14

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.62559	0.058
Mature Green Tomato/Ripe Tomato	2.01207	0.036
Immature Eggplant/Mature Eggplant	0.57832	0.068
Ripe Pepper/Ripe Tomato	0.53816	0.224
Mature Eggplant/Ripe Tomato	5.86503	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0449
12-2/M82	N/A	N/A
12-4/M82	1.13963	1
1-3/M82	N/A	N/A
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	0.88742
4-1-1/M82	N/A	N/A
4-1/M82	1.89321
4-3-2/M82	N/A	N/A
4-3/M82	0.6741
5-3/M82	0.99592
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.96694
7-2/M82	N/A	N/A
9-3-2/M82	1.27104	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.38164	0.277
IL2-6/WTpooled	1.04368	1
IL7-5/WTpooled	0.89511	1
IL7-3/WTpooled	1.08722	1
IL12-4/WTpooled	0.99846	1
IL1-4/WTpooled	1.09801	1
WT/WTpooled	0.99779	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	1.21336	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08063	0.921
DC3000/delta hrp 6h	1.01663	0.95
DC3000/delta hrp 12h	1.83748	1
DC3000/delta hrp 24h	0.961	0.682

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.00765	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88334	1
Exp 36h	0.8827	0.82
Exp 60h	0.82352	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97824	1
Var 0h	1.10896	0.936
Var 12h I row2-row1	0.96584	0.948
Var 12h NI row2-row1	1.0753	1
Var 36h I row2-row1	1.19473	0.298
Var 36h NI row2-row1	1.06766	1
Var 60h I row2-row1	1.0145	1
Var 60h NI row2-row1	0.91353	0.818
Time course 0hI-0hNI	0.91554	0.325
Time course 12hI-12hNI	1.0909	0.452
Time course 36hI-36hNI	1.12057	0.355
Time course 60hI-60hNI	1.19469	0.053

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)	0.76812	0.22
transgenic ySAMdc/azygous control (breaker)	0.72396	0.131
transgenic ySAMdc/azygous control (red)	0.82487	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10374	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30252	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.56512	0.172
Manapal/WT (break)	0.95354	1
Manapal/WT (red)	0.80553	0.181