Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.1.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12006	0.561
27DAP/17DAP	1.0575	0.877
39DAP/27DAP	0.98071	0.749
41DAP/39DAP	1.00875	1
42DAP/41DAP	0.93695	1
43DAP/42DAP	1.02107	1
47DAP/43DAP	1.05467	0.926
52DAP/47DAP	0.97821	0.908
57DAP/52DAP	1.06114	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27038	0.04
17DAP/reference	1.29033	0.049
27DAP/reference	1.2211	0.091
39DAP/reference	1.11754	0.318
41DAP/reference	1.50958	0.036
42DAP/reference	1.45107	0.001
43DAP/reference	1.25701	0.133
47DAP/reference	1.19995	0.005
52DAP/reference	1.20631	0.371
57DAP/reference	0.91534	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95853	0.526
27DAP/17DAP	1.05542
39DAP/27DAP	1.06513
41DAP/39DAP	0.9934	1
42DAP/41DAP	0.96624	0.734
43DAP/42DAP	1.00649	0.83
47DAP/43DAP	0.9686	0.87
52DAP/47DAP	1.00607	1
57DAP/52DAP	0.99016	0.828
57DAP/7DAP	1.01106	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01103	1
17DAP/reference	1.08419	0.328
27DAP/reference	0.99717	0.748
39DAP/reference	1.00709	0.909
41DAP/reference	0.9974	0.778
42DAP/reference	1.05252	0.03
43DAP/reference	0.99973	0.727
47DAP/reference	1.18442	0.205
52DAP/reference	0.93865	0.332
57DAP/reference	0.9914	0.589

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37117	0.049
17DAP/reference	1.80268	0.007
27DAP/reference	1.42707	0.02
39DAP/reference	1.28097	0.018
41DAP/reference	1.48096	0.008
42DAP/reference	1.32003	0.057
43DAP/reference	1.63175	0.111
47DAP/reference	1.31008	0.008
52DAP/reference	1.75118	0.006
57DAP/reference	1.84954	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02199	0.918
17DAP/reference	1.11845	0.551
27DAP/reference	0.94072	0.195
39DAP/reference	1.11352	0.437
41DAP/reference	0.9516	0.033
42DAP/reference	1.08725	0.701
43DAP/reference	1.06347	0.84
47DAP/reference	1.32228	0.077
52DAP/reference	0.95394	0.637
57DAP/reference	0.7349	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97212	1
26DAP/20DAP	1.01853	1
34DAP/26DAP	0.97916	0.97
51DAP/34DAP	1.01101	0.898
52DAP/51DAP	1.00061	1
53DAP/52DAP	1.01943	0.944
55DAP/53DAP	0.92286
57DAP/55DAP	1.03438	0.975
62DAP/57DAP	1.08461	1
68DAP/62DAP	0.60441	0.579
68DAP/14DAP	0.89882	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12764	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97053	0.66
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.5735

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.23515	0.551
1-1-2/M82	0.9758	1
12-2/M82	0.88329	0.721
12-4/M82	1.04022	1
1-3/M82	1.05677	0.479
2-1-1/M82	1.11082	0.764
2-1/M82	N/A	N/A
2-6/M82	0.97698	1
3-2/M82	0.97668	1
4-1-1/M82	1.05453	1
4-1/M82	1.11547	1
4-3-2/M82	1.05265
4-3/M82	0.95789	0.72
5-3/M82	1.02337	1
6-2/M82	1.03265	1
6-3/M82	0.98628	1
7-1/M82	1.04438	0.598
7-2/M82	1.03594	1
9-3-2/M82	0.81921	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.3335	0.277
IL2-6/WTpooled	0.88632	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0096	1
IL12-4/WTpooled	0.72871	0.52
IL1-4/WTpooled	1.19012	1
WT/WTpooled	1.04613	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	0.70951

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11379	0.894
DC3000/delta hrp 6h	0.75657	0.95
DC3000/delta hrp 12h	1.03116	1
DC3000/delta hrp 24h	0.98056	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21319	0.042
DC3000 delta B/DC3000 delta AB	1.15092	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02829	1
Exp 36h	0.50867	0.313
Exp 60h	1.13636	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97514	1
Var 0h	0.93732	1
Var 12h I row2-row1	1.18595	0.254
Var 12h NI row2-row1	0.91196	0.82
Var 36h I row2-row1	0.7892	0.805
Var 36h NI row2-row1	1.0482	1
Var 60h I row2-row1	1.16434	1
Var 60h NI row2-row1	1.07577	1
Time course 0hI-0hNI	1.05403	1
Time course 12hI-12hNI	0.96786	0.769
Time course 36hI-36hNI	0.96115	0.433
Time course 60hI-60hNI	1.24716	0.069

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)	0.95483	0.662
transgenic ySAMdc/azygous control (breaker)	1.10885	1
transgenic ySAMdc/azygous control (red)	0.87762	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95537	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27969	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07622	0.307
Manapal/WT (break)	1.02049	1
Manapal/WT (red)	1.01661	1