Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09756	0.656
27DAP/17DAP	1.09756	0.881
39DAP/27DAP	0.97746	0.608
41DAP/39DAP	1.18445	0.473
42DAP/41DAP	1.21624	0.722
43DAP/42DAP	0.92438	0.807
47DAP/43DAP	1.00328	0.934
52DAP/47DAP	1.06978	0.898
57DAP/52DAP	1.0005	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97509	0.539
17DAP/reference	0.81843	0.013
27DAP/reference	1.07004	0.468
39DAP/reference	1.14606	0.191
41DAP/reference	0.74124	0.039
42DAP/reference	0.88099	0.041
43DAP/reference	0.93853	0.519
47DAP/reference	0.92927	0.242
52DAP/reference	1.13888	0.43
57DAP/reference	1.16669	0.043

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86292	0.442
27DAP/17DAP	0.96433	0.724
39DAP/27DAP	1.03411	0.77
41DAP/39DAP	1.04826	0.876
42DAP/41DAP	0.94117	0.625
43DAP/42DAP	0.99049	0.928
47DAP/43DAP	0.96003	0.823
52DAP/47DAP	1.10299	0.71
57DAP/52DAP	1.01583	1
57DAP/7DAP	0.97032	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05268	0.98
17DAP/reference	1.07458	0.627
27DAP/reference	0.85025	0.066
39DAP/reference	1.10922	0.314
41DAP/reference	0.75656	0.043
42DAP/reference	0.87278	0.16
43DAP/reference	1.11799	0.707
47DAP/reference	1.03725	0.837
52DAP/reference	1.01187	1
57DAP/reference	0.99634	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92272	0.386
17DAP/reference	0.93975	0.357
27DAP/reference	1.03512	0.79
39DAP/reference	1.07158	0.377
41DAP/reference	1.26036	0.031
42DAP/reference	1.09132	0.476
43DAP/reference	1.01619	0.801
47DAP/reference	0.92217	0.062
52DAP/reference	0.95574	0.327
57DAP/reference	0.90095	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9404	0.362
17DAP/reference	0.87052	0.189
27DAP/reference	0.92999	0.319
39DAP/reference	0.94465	0.111
41DAP/reference	0.85746	0.209
42DAP/reference	0.90085	0.361
43DAP/reference	0.93894	0.416
47DAP/reference	0.87014	0.139
52DAP/reference	0.80553	0.228
57DAP/reference	1.17405	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.66104	0.159
26DAP/20DAP	1.05371	1
34DAP/26DAP	1.06925	1
51DAP/34DAP	1.01816	0.988
52DAP/51DAP	1.29194	0.09
53DAP/52DAP	0.91783	0.703
55DAP/53DAP	1.14925	0.387
57DAP/55DAP	0.9459	0.724
62DAP/57DAP	1.25188	0.902
68DAP/62DAP	1.04984	0.858
68DAP/14DAP	0.98319	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91195	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.00162	0.068
Mature Green Tomato/Ripe Tomato	1.09834	0.948
Immature Eggplant/Mature Eggplant	1.59488	0.05
Ripe Pepper/Ripe Tomato	0.51546	0.224
Mature Eggplant/Ripe Tomato	0.90203	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.24467	0.742
1-1-2/M82	1.03339	1
12-2/M82	0.94664
12-4/M82	1.02497	1
1-3/M82	0.81267
2-1-1/M82	0.7426
2-1/M82	N/A	N/A
2-6/M82	0.89883
3-2/M82	1.10353	0.967
4-1-1/M82	0.95874	1
4-1/M82	1.05503	1
4-3-2/M82	0.94893	1
4-3/M82	0.97378	1
5-3/M82	1.01147	1
6-2/M82	N/A	N/A
6-3/M82	0.97557	1
7-1/M82	1.09811
7-2/M82	1.28194
9-3-2/M82	1.2216	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19996	0.493
IL2-6/WTpooled	1.08365	0.788
IL7-5/WTpooled	0.28911
IL7-3/WTpooled	0.94668	1
IL12-4/WTpooled	0.83509	0.71
IL1-4/WTpooled	1.22234	1
WT/WTpooled	0.89709	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	0.98396	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14937	0.846
DC3000/delta hrp 6h	0.95634	0.95
DC3000/delta hrp 12h	1.22902	1
DC3000/delta hrp 24h	0.86905	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88083	0.232
DC3000 delta B/DC3000 delta AB	1.01151	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78374	1
Exp 36h	0.9392	0.879
Exp 60h	0.8843	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00306	1
Var 0h	1.06621	0.98
Var 12h I row2-row1	0.96299	0.856
Var 12h NI row2-row1	0.97041	0.82
Var 36h I row2-row1	0.8874	0.202
Var 36h NI row2-row1	0.96096	0.645
Var 60h I row2-row1	1.36408	1
Var 60h NI row2-row1	1.06205	0.904
Time course 0hI-0hNI	1.11674	0.297
Time course 12hI-12hNI	1.011	0.9
Time course 36hI-36hNI	1.04596	0.453
Time course 60hI-60hNI	1.31699	0.008

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)	0.94716	0.567
transgenic ySAMdc/azygous control (breaker)	0.60134	0.134
transgenic ySAMdc/azygous control (red)	0.98074	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98754	0.486

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94593	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03208	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.58146	0.181