Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07191	0.947
27DAP/17DAP	1.26164	0.742
39DAP/27DAP	0.74636	0.301
41DAP/39DAP	1.03734	0.985
42DAP/41DAP	1.10226	0.978
43DAP/42DAP	1.24045	0.772
47DAP/43DAP	1.23251	0.527
52DAP/47DAP	1.35185	0.665
57DAP/52DAP	1.20127	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90902	0.136
17DAP/reference	0.92273	0.038
27DAP/reference	0.97838	0.623
39DAP/reference	1.00483	1
41DAP/reference	0.8356	0.039
42DAP/reference	0.81709	0.006
43DAP/reference	0.93909	0.273
47DAP/reference	0.99944	0.72
52DAP/reference	1.0925	0.096
57DAP/reference	1.09449	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37296	0.068
27DAP/17DAP	0.85665	0.508
39DAP/27DAP	1.31909	0.532
41DAP/39DAP	0.94299	0.849
42DAP/41DAP	1.46113	0.334
43DAP/42DAP	1.02392	0.83
47DAP/43DAP	0.99905	0.99
52DAP/47DAP	1.14047	0.589
57DAP/52DAP	1.10142	0.759
57DAP/7DAP	1.17382	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20637	0.298
17DAP/reference	1.09102	0.437
27DAP/reference	1.01422	0.8
39DAP/reference	0.96698	0.411
41DAP/reference	1.22799	0.141
42DAP/reference	1.05201	0.889
43DAP/reference	1.13596	0.432
47DAP/reference	0.99905	1
52DAP/reference	1.18419	0.229
57DAP/reference	1.18235	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84082	0.145
17DAP/reference	0.84102	0.047
27DAP/reference	0.87761	0.134
39DAP/reference	0.8907	0.095
41DAP/reference	0.8832	0.118
42DAP/reference	0.77755	0.019
43DAP/reference	0.85557	0.095
47DAP/reference	0.83068	0.054
52DAP/reference	0.89192	0.22
57DAP/reference	0.83362	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09612	0.709
17DAP/reference	1.02714	1
27DAP/reference	1.32559	0.052
39DAP/reference	1.20211	0.175
41DAP/reference	1.04884	0.916
42DAP/reference	0.98256	0.816
43DAP/reference	1.00951	0.738
47DAP/reference	1.05832	0.405
52DAP/reference	1.09854	0.614
57DAP/reference	1.15855	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93774	1
26DAP/20DAP	1.58676	0.238
34DAP/26DAP	1.02561	1
51DAP/34DAP	2.19828	0.034
52DAP/51DAP	1.037	0.848
53DAP/52DAP	1.13666	0.166
55DAP/53DAP	0.71664	0.055
57DAP/55DAP	1.10922	1
62DAP/57DAP	0.97782	0.871
68DAP/62DAP	1.29658	0.214
68DAP/14DAP	2.2182	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.48344	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.5431	0.107
Mature Green Tomato/Ripe Tomato	0.79602	0.287
Immature Eggplant/Mature Eggplant	1.11899	0.288
Ripe Pepper/Ripe Tomato	1.32562	1
Mature Eggplant/Ripe Tomato	0.57481	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11129	0.742
1-1-2/M82	1.06538	1
12-2/M82	1.03822	1
12-4/M82	1.04906	1
1-3/M82	0.86994	0.378
2-1-1/M82	1.21208	0.457
2-1/M82	1.1016	1
2-6/M82	0.99594	1
3-2/M82	0.94915	0.752
4-1-1/M82	0.9713	1
4-1/M82	1.27423	0.853
4-3-2/M82	0.95949	1
4-3/M82	1.1915	1
5-3/M82	0.95595	0.642
6-2/M82	1.1421	1
6-3/M82	1.04843	1
7-1/M82	1.06054	1
7-2/M82	1.14812	0.324
9-3-2/M82	1.23839	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.43006	0.365
IL2-6/WTpooled	0.94465	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.47595	1
IL12-4/WTpooled	1.16951	0.695
IL1-4/WTpooled	1.40571	1
WT/WTpooled	1.02047	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	0.91686	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92172	0.868
DC3000/delta hrp 6h	1.10508	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.88378	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95103	0.629
DC3000 delta B/DC3000 delta AB	1.00907	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89779	1
Exp 36h	0.90333	0.749
Exp 60h	0.89959	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04165	1
Var 0h	0.98281	1
Var 12h I row2-row1	1.05661	0.692
Var 12h NI row2-row1	1.23245	0.649
Var 36h I row2-row1	1.17699	0.908
Var 36h NI row2-row1	1.48404	0.482
Var 60h I row2-row1	0.73821	0.285
Var 60h NI row2-row1	1.3283	0.904
Time course 0hI-0hNI	0.9776	0.9
Time course 12hI-12hNI	1.04506	0.788
Time course 36hI-36hNI	0.98792	0.644
Time course 60hI-60hNI	0.61363	0.015

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)	0.93448	0.454
transgenic ySAMdc/azygous control (breaker)	0.87041	0.49
transgenic ySAMdc/azygous control (red)	1.15409	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10987	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45984	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49786	0.105
Manapal/WT (break)	1.18831	0.381
Manapal/WT (red)	1.18385	0.164