Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91025	0.511
27DAP/17DAP	1.0111	0.964
39DAP/27DAP	0.97299	0.7
41DAP/39DAP	1.13243	0.722
42DAP/41DAP	1.40597	0.642
43DAP/42DAP	1.03602	0.937
47DAP/43DAP	0.99683	0.943
52DAP/47DAP	0.7551	0.403
57DAP/52DAP	0.86264	0.768

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96508	0.476
17DAP/reference	1.0935	0.178
27DAP/reference	0.97166	0.595
39DAP/reference	1.03052	0.615
41DAP/reference	1.13089	0.058
42DAP/reference	0.85576	0.008
43DAP/reference	0.99379	0.861
47DAP/reference	0.90744	0.025
52DAP/reference	0.78516	0.033
57DAP/reference	0.86545	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94149	0.388
27DAP/17DAP	1.00137	1
39DAP/27DAP	1.05139	0.553
41DAP/39DAP	1.03755	0.887
42DAP/41DAP	0.93352	0.495
43DAP/42DAP	1.10502	0.094
47DAP/43DAP	0.98883	0.939
52DAP/47DAP	1.00829	0.979
57DAP/52DAP	0.98673	0.793
57DAP/7DAP	1.05045	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88441	0.073
17DAP/reference	0.86089	0.013
27DAP/reference	0.86084	0.01
39DAP/reference	0.93976	0.073
41DAP/reference	0.95204	0.166
42DAP/reference	0.97013	0.338
43DAP/reference	0.85423	0.013
47DAP/reference	0.90175	0.044
52DAP/reference	0.89206	0.021
57DAP/reference	0.83924	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01957	0.787
17DAP/reference	1.02185	0.924
27DAP/reference	0.90183	0.212
39DAP/reference	0.8117	0.108
41DAP/reference	0.7488	0.016
42DAP/reference	0.8006	0.042
43DAP/reference	0.98571	0.633
47DAP/reference	0.93337	0.036
52DAP/reference	0.95587	0.28
57DAP/reference	1.14321	0.387

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8685	0.044
17DAP/reference	0.99289	0.778
27DAP/reference	0.85551	0.035
39DAP/reference	0.83202	0.01
41DAP/reference	0.87788	0.019
42DAP/reference	0.80657	0.019
43DAP/reference	0.74148	0.061
47DAP/reference	0.8908	0.224
52DAP/reference	0.84027	0.109
57DAP/reference	0.57936	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01733	1
26DAP/20DAP	0.90361	0.512
34DAP/26DAP	1.11533	0.819
51DAP/34DAP	0.96528	0.743
52DAP/51DAP	0.99018	1
53DAP/52DAP	1.04167	0.868
55DAP/53DAP	1.00051	1
57DAP/55DAP	0.98068	0.88
62DAP/57DAP	1.15974	0.678
68DAP/62DAP	0.96003	0.787
68DAP/14DAP	1.21881	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88439	0.037

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.57443	0.063
Mature Green Tomato/Ripe Tomato	1.50565	0.814
Immature Eggplant/Mature Eggplant	0.45441	0.062
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	5.87634

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06048	1
1-1-2/M82	0.99244	1
12-2/M82	1.05392	1
12-4/M82	0.93322	1
1-3/M82	0.87278	0.501
2-1-1/M82	1.32964	0.689
2-1/M82	1.01935	1
2-6/M82	1.10595	0.594
3-2/M82	0.98933
4-1-1/M82	0.98726	1
4-1/M82	1.19657
4-3-2/M82	0.84364	0.698
4-3/M82	0.96509	1
5-3/M82	0.92946	1
6-2/M82	1.08677	1
6-3/M82	0.98113	1
7-1/M82	1.06465	0.87
7-2/M82	1.00018	1
9-3-2/M82	1.05509

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69219
IL2-6/WTpooled	1.11657	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05538	1
IL12-4/WTpooled	1.02964	1
IL1-4/WTpooled	1.20795	1
WT/WTpooled	1.06938	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	0.67914	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99146
DC3000/delta hrp 6h	0.95849	0.95
DC3000/delta hrp 12h	0.9605	1
DC3000/delta hrp 24h	0.90901	0.231

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04663	0.476
DC3000 delta B/DC3000 delta AB	0.98322	0.892

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84772	1
Exp 36h	0.737	0.321
Exp 60h	0.59136	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99696	1
Var 0h	0.83299	0.933
Var 12h I row2-row1	0.82765	0.357
Var 12h NI row2-row1	0.94606	0.82
Var 36h I row2-row1	0.98745	1
Var 36h NI row2-row1	1.08462	1
Var 60h I row2-row1	1.57013	1
Var 60h NI row2-row1	1.05866	0.904
Time course 0hI-0hNI	1.02553	0.852
Time course 12hI-12hNI	0.97547	0.705
Time course 36hI-36hNI	0.80603	0.028
Time course 60hI-60hNI	0.52132	0.006

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)	1.38158	0.261
transgenic ySAMdc/azygous control (breaker)	1.80978	0.161
transgenic ySAMdc/azygous control (red)	1.29108	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95216	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.33336	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.15524	0.14
Manapal/WT (break)	2.64985	0.126
Manapal/WT (red)	2.67159	0.137