Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86228	0.182
27DAP/17DAP	0.81564	0.572
39DAP/27DAP	1.08311	1
41DAP/39DAP	1.15887	0.447
42DAP/41DAP	1.18196	0.877
43DAP/42DAP	1.06205	0.937
47DAP/43DAP	0.98914	0.879
52DAP/47DAP	1.11687	0.847
57DAP/52DAP	0.93587	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9981	0.727
17DAP/reference	0.907	0.046
27DAP/reference	0.94706	0.176
39DAP/reference	0.99545	0.921
41DAP/reference	0.95157	0.341
42DAP/reference	0.96946	0.196
43DAP/reference	0.9751	0.594
47DAP/reference	1.00138	0.72
52DAP/reference	0.99437	0.668
57DAP/reference	0.90958	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13433	0.455
27DAP/17DAP	0.99692	0.969
39DAP/27DAP	1.11149	0.41
41DAP/39DAP	0.9457	0.893
42DAP/41DAP	0.98159	0.816
43DAP/42DAP	1.24934	0.024
47DAP/43DAP	0.9446	0.382
52DAP/47DAP	0.87659	0.334
57DAP/52DAP	0.8769	0.531
57DAP/7DAP	0.98538	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90431	0.1
17DAP/reference	0.93934	0.167
27DAP/reference	0.99743	0.748
39DAP/reference	0.97736	0.411
41DAP/reference	0.89964	0.07
42DAP/reference	1.0163	0.686
43DAP/reference	0.98414	0.48
47DAP/reference	0.8566	0.066
52DAP/reference	0.89434	0.027
57DAP/reference	1.04209	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06609	0.516
17DAP/reference	1.04915	0.658
27DAP/reference	0.98589	0.619
39DAP/reference	0.97055	0.469
41DAP/reference	0.98262	0.481
42DAP/reference	0.91525	0.098
43DAP/reference	1.06837	0.745
47DAP/reference	0.90893	0.116
52DAP/reference	0.98051	0.407
57DAP/reference	1.04659	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93064	0.127
17DAP/reference	0.97006	0.452
27DAP/reference	0.93316	0.23
39DAP/reference	0.91157	0.009
41DAP/reference	1.13416	0.031
42DAP/reference	1.21624	0.024
43DAP/reference	1.08343	0.28
47DAP/reference	0.77726	0.005
52DAP/reference	1.03624	0.862
57DAP/reference	0.79527	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86743	0.672
26DAP/20DAP	0.94399	1
34DAP/26DAP	1.05939	1
51DAP/34DAP	0.93323	0.606
52DAP/51DAP	1.14656	0.111
53DAP/52DAP	1.05931	0.806
55DAP/53DAP	1.01684	1
57DAP/55DAP	0.9335	0.709
62DAP/57DAP	0.94098	0.994
68DAP/62DAP	0.70562	0.055
68DAP/14DAP	0.90117	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99818	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.95711	0.058
Mature Green Tomato/Ripe Tomato	0.93409	0.522
Immature Eggplant/Mature Eggplant	0.65017	0.064
Ripe Pepper/Ripe Tomato	0.78336	1
Mature Eggplant/Ripe Tomato	0.38554	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97611	0.944
1-1-2/M82	0.90249	0.754
12-2/M82	N/A	N/A
12-4/M82	0.96229	1
1-3/M82	0.64329	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.14452	0.695
3-2/M82	0.85197	0.752
4-1-1/M82	1.13557	1
4-1/M82	1.023	1
4-3-2/M82	0.93026	1
4-3/M82	0.96697	1
5-3/M82	0.99222	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.02296	N/A
9-3-2/M82	0.85876	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.89092	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03052	1
IL12-4/WTpooled	0.97316	1
IL1-4/WTpooled	0.97295	1
WT/WTpooled	1.00646	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	0.7276	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95947	1
DC3000/delta hrp 6h	1.0727	1
DC3000/delta hrp 12h	0.95498	1
DC3000/delta hrp 24h	1.74545	0.026

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03431	0.408
DC3000 delta B/DC3000 delta AB	1.06039	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12854	1
Exp 36h	1.02682	1
Exp 60h	1.06629	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04829	1
Var 0h	0.76946	0.936
Var 12h I row2-row1	0.8571	0.338
Var 12h NI row2-row1	0.98005	0.906
Var 36h I row2-row1	0.82351	1
Var 36h NI row2-row1	1.14476	0.482
Var 60h I row2-row1	0.92211	0.832
Var 60h NI row2-row1	1.03713	1
Time course 0hI-0hNI	0.93784	0.552
Time course 12hI-12hNI	1.01169	0.82
Time course 36hI-36hNI	0.97051	0.433
Time course 60hI-60hNI	0.60517	0.007

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)	1.01482	0.748
transgenic ySAMdc/azygous control (breaker)	0.7855	0.132
transgenic ySAMdc/azygous control (red)	1.14684	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04944	0.037

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01368	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.39045	0.096
Manapal/WT (break)	2.30599	0.126
Manapal/WT (red)	2.94874	0.133