Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12569	0.893
27DAP/17DAP	1.19192	0.845
39DAP/27DAP	0.86213	0.462
41DAP/39DAP	1.55515	0.264
42DAP/41DAP	1.11812	1
43DAP/42DAP	0.94484	0.887
47DAP/43DAP	1.03615	0.972
52DAP/47DAP	1.32512	0.498
57DAP/52DAP	1.01394	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97153	0.526
17DAP/reference	0.92724	0.158
27DAP/reference	0.95072	0.457
39DAP/reference	0.94715	0.5
41DAP/reference	0.92861	0.267
42DAP/reference	0.92915	0.069
43DAP/reference	0.9992	0.882
47DAP/reference	1.00954	1
52DAP/reference	1.16756	0.128
57DAP/reference	1.1713	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9397	0.56
27DAP/17DAP	1.05152	0.912
39DAP/27DAP	1.06274	0.534
41DAP/39DAP	1.05026	0.914
42DAP/41DAP	0.83125	0.096
43DAP/42DAP	1.15616	0.086
47DAP/43DAP	1.01424	0.969
52DAP/47DAP	0.96824	0.857
57DAP/52DAP	0.94551	0.596
57DAP/7DAP	1.13812	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84663	0.095
17DAP/reference	0.77997	0.011
27DAP/reference	0.78092	0.01
39DAP/reference	0.81915	0.027
41DAP/reference	0.92696	0.174
42DAP/reference	0.79463	0.018
43DAP/reference	0.72424	0.011
47DAP/reference	0.80417	0.066
52DAP/reference	0.7967	0.038
57DAP/reference	0.89357	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9058	0.238
17DAP/reference	0.83413	0.012
27DAP/reference	0.98269	0.554
39DAP/reference	1.05951	0.956
41DAP/reference	0.98926	0.545
42DAP/reference	1.73176	0.351
43DAP/reference	0.98906	0.681
47DAP/reference	0.86992	0.036
52DAP/reference	1.04264	0.667
57DAP/reference	0.84022	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79979	0.039
17DAP/reference	0.9945	0.763
27DAP/reference	0.74837	0.047
39DAP/reference	0.87067	0.133
41DAP/reference	1.02225	0.984
42DAP/reference	0.82217	0.071
43DAP/reference	0.88791	0.079
47DAP/reference	1.0455	0.562
52DAP/reference	0.81319	0.232
57DAP/reference	1.19038	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.53652	0.966
26DAP/20DAP	0.76065	0.244
34DAP/26DAP	1.01557	1
51DAP/34DAP	1.2646	0.483
52DAP/51DAP	1.05971	0.662
53DAP/52DAP	1.0301	0.868
55DAP/53DAP	1.03604	0.898
57DAP/55DAP	0.99971	0.904
62DAP/57DAP	1.00824	1
68DAP/62DAP	1.1865	0.664
68DAP/14DAP	0.94712	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80257	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.05658	1
Immature Eggplant/Mature Eggplant	2.08582	0.088
Ripe Pepper/Ripe Tomato	0.63685
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.92055	1
12-2/M82	N/A	N/A
12-4/M82	0.91602	1
1-3/M82	0.74716	0.501
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	1.02216
4-1-1/M82	N/A	N/A
4-1/M82	0.82277	1
4-3-2/M82	0.74327
4-3/M82	N/A	N/A
5-3/M82	1.08507	1
6-2/M82	0.8741
6-3/M82	N/A	N/A
7-1/M82	1.00389
7-2/M82	1.00731	1
9-3-2/M82	0.98567	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99846	1
IL2-6/WTpooled	1.16707	0.788
IL7-5/WTpooled	1.71137	0.792
IL7-3/WTpooled	1.14931	1
IL12-4/WTpooled	1.05431	0.785
IL1-4/WTpooled	1.0771	1
WT/WTpooled	1.03061	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	0.87076

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98268	1
DC3000/delta hrp 6h	1.07091	1
DC3000/delta hrp 12h	0.88629	1
DC3000/delta hrp 24h	1.11416	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52066
DC3000 delta B/DC3000 delta AB	1.2882	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.92561	0.82
Exp 60h	1.27094	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10679	1
Var 0h	0.45318	1
Var 12h I row2-row1	1.06266	0.506
Var 12h NI row2-row1	0.90229	0.82
Var 36h I row2-row1	0.8545	0.438
Var 36h NI row2-row1	0.8782	0.522
Var 60h I row2-row1	1.36684	0.562
Var 60h NI row2-row1	1.3161	0.904
Time course 0hI-0hNI	1.11443	0.603
Time course 12hI-12hNI	0.99976	1
Time course 36hI-36hNI	0.94867	0.142
Time course 60hI-60hNI	2.10876	0.047

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)	0.90163	0.529
transgenic ySAMdc/azygous control (breaker)	1.09975	1
transgenic ySAMdc/azygous control (red)	0.99426	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1645	0.041

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86889	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.53571	0.172
Manapal/WT (break)	0.75709	0.333
Manapal/WT (red)	2.63171	0.413