Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.17.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95281	0.699
27DAP/17DAP	1.80995	0.749
39DAP/27DAP	1.18756	0.894
41DAP/39DAP	1.04059	1
42DAP/41DAP	0.83026	1
43DAP/42DAP	0.95785	0.892
47DAP/43DAP	1.03203	0.904
52DAP/47DAP	0.93368	0.783
57DAP/52DAP	1.06106	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96284	0.476
17DAP/reference	0.8463	0.043
27DAP/reference	0.94551	0.428
39DAP/reference	0.89783	0.35
41DAP/reference	0.78814	0.031
42DAP/reference	0.96369	0.225
43DAP/reference	0.82844	0.073
47DAP/reference	1.00956	0.72
52DAP/reference	1.1263	0.286
57DAP/reference	1.05859	0.6

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99732	0.871
27DAP/17DAP	0.95957	0.878
39DAP/27DAP	0.89895	0.287
41DAP/39DAP	1.0021	1
42DAP/41DAP	1.10453	0.74
43DAP/42DAP	0.90862	0.415
47DAP/43DAP	1.07893	0.865
52DAP/47DAP	0.80849	0.575
57DAP/52DAP	0.98792	0.789
57DAP/7DAP	1.31577	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9131	0.146
17DAP/reference	0.97447	0.447
27DAP/reference	1.06945	0.664
39DAP/reference	0.6984	0.031
41DAP/reference	0.76332	0.034
42DAP/reference	0.76022	0.021
43DAP/reference	0.82418	0.056
47DAP/reference	1.10837	0.761
52DAP/reference	0.84082	0.057
57DAP/reference	0.8858	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82279	0.124
17DAP/reference	0.88811	0.153
27DAP/reference	1.10426	0.618
39DAP/reference	1.04042	0.702
41DAP/reference	1.031	1
42DAP/reference	1.04805	0.61
43DAP/reference	0.96672	0.552
47DAP/reference	0.89026	0.092
52DAP/reference	1.04084	1
57DAP/reference	0.7951	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92172	0.268
17DAP/reference	0.8562	0.3
27DAP/reference	0.92578	0.286
39DAP/reference	0.95396	0.43
41DAP/reference	1.01691	1
42DAP/reference	1.16845	0.45
43DAP/reference	1.01684	0.827
47DAP/reference	1.16767	0.12
52DAP/reference	0.94761	0.611
57DAP/reference	1.39712	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10142	0.966
26DAP/20DAP	1.1495	0.988
34DAP/26DAP	0.95014	0.898
51DAP/34DAP	0.89005	0.508
52DAP/51DAP	0.913	1
53DAP/52DAP	0.95434	0.797
55DAP/53DAP	0.9609	0.761
57DAP/55DAP	1.18356	0.881
62DAP/57DAP	1.26211	0.678
68DAP/62DAP	0.54721	0.543
68DAP/14DAP	0.64853

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67728	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55419
Mature Green Tomato/Ripe Tomato	1.02662	0.881
Immature Eggplant/Mature Eggplant	1.45563
Ripe Pepper/Ripe Tomato	0.55669	0.224
Mature Eggplant/Ripe Tomato	0.37633	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99497	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.91848	0.282
1-3/M82	1.47533	0.479
2-1-1/M82	0.66723
2-1/M82	1.4167
2-6/M82	1.01239	1
3-2/M82	0.9059
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.14944
5-3/M82	1.09509	1
6-2/M82	N/A	N/A
6-3/M82	0.83062	1
7-1/M82	1.2915
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10512	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.26276
IL12-4/WTpooled	1.22617	0.646
IL1-4/WTpooled	1.09933	0.426
WT/WTpooled	0.93059	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	0.96713	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90302	0.868
DC3000/delta hrp 6h	0.85521	0.95
DC3000/delta hrp 12h	1.04335	1
DC3000/delta hrp 24h	1.00988	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04504	1
DC3000 delta B/DC3000 delta AB	1.30266	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04559	0.254
Exp 36h	1.21512	1
Exp 60h	1.1394	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01296	1
Var 0h	0.87479	1
Var 12h I row2-row1	1.00401	1
Var 12h NI row2-row1	1.21524	0.281
Var 36h I row2-row1	1.05461	1
Var 36h NI row2-row1	0.89081	0.549
Var 60h I row2-row1	0.82918	0.439
Var 60h NI row2-row1	0.83047	0.756
Time course 0hI-0hNI	1.06774	0.764
Time course 12hI-12hNI	0.97711	0.874
Time course 36hI-36hNI	1.09144	0.881
Time course 60hI-60hNI	1.36412	0.009

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)	1.05156	0.699
transgenic ySAMdc/azygous control (breaker)	1.16859	1
transgenic ySAMdc/azygous control (red)	0.99332	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04463	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01144	1
Manapal/WT (break)	0.95589	1
Manapal/WT (red)	1.1117	1