Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.12.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84812	0.166
27DAP/17DAP	1.14984	0.857
39DAP/27DAP	1.31862	0.405
41DAP/39DAP	0.73432	0.171
42DAP/41DAP	1.42234	0.712
43DAP/42DAP	0.94183	0.877
47DAP/43DAP	0.78096	0.355
52DAP/47DAP	0.94611	0.845
57DAP/52DAP	0.82909	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26391	0.188
17DAP/reference	2.26793	0.044
27DAP/reference	3.70427	0.008
39DAP/reference	1.66123	0.04
41DAP/reference	2.69366	0.013
42DAP/reference	1.25375	0.021
43DAP/reference	0.83413	0.016
47DAP/reference	0.68053	0.003
52DAP/reference	0.61265	0.013
57DAP/reference	0.7611	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17065	0.431
27DAP/17DAP	0.97594	0.943
39DAP/27DAP	0.92872	0.601
41DAP/39DAP	1.0886	0.837
42DAP/41DAP	0.94832	0.635
43DAP/42DAP	0.81843	0.068
47DAP/43DAP	1.09001	0.529
52DAP/47DAP	0.9361	0.634
57DAP/52DAP	0.99397	0.833
57DAP/7DAP	1.10369	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84827	0.183
17DAP/reference	0.93096	0.253
27DAP/reference	0.99677	0.53
39DAP/reference	0.99409	0.64
41DAP/reference	1.29514	0.701
42DAP/reference	1.05956	0.686
43DAP/reference	0.97248	0.459
47DAP/reference	1.22509	0.776
52DAP/reference	1.08617	0.732
57DAP/reference	1.14926	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09976	0.577
17DAP/reference	3.79526	0.006
27DAP/reference	3.44518	0.012
39DAP/reference	3.48811	0.011
41DAP/reference	2.80515	0.005
42DAP/reference	5.19766	0.007
43DAP/reference	1.88398	0.161
47DAP/reference	2.18737	0.01
52DAP/reference	4.00285	0.006
57DAP/reference	2.01683	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17809	0.882
17DAP/reference	1.68847	0.283
27DAP/reference	1.80847
39DAP/reference	1.31272	0.39
41DAP/reference	1.17601	0.554
42DAP/reference	1.2925	0.194
43DAP/reference	0.94231	0.449
47DAP/reference	0.71685	0.005
52DAP/reference	0.82387	0.327
57DAP/reference	0.72697	0.055

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96338	1
26DAP/20DAP	0.95083	1
34DAP/26DAP	0.99548	1
51DAP/34DAP	1.25773	0.785
52DAP/51DAP	0.89781	1
53DAP/52DAP	1.28533	0.187
55DAP/53DAP	1.17307	0.693
57DAP/55DAP	1.01315	0.953
62DAP/57DAP	0.91407	0.681
68DAP/62DAP	1.04798	0.944
68DAP/14DAP	0.45201	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25374	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.35695	0.064
Immature Eggplant/Mature Eggplant	0.73937	0.067
Ripe Pepper/Ripe Tomato	0.42806
Mature Eggplant/Ripe Tomato	6.75746	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	2.49184
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
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	0.73574
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.04744	0.241
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.74601
7-2/M82	N/A	N/A
9-3-2/M82	1.74899	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.23731	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12503	0.758
DC3000/delta hrp 6h	0.97936	0.95
DC3000/delta hrp 12h	1.0144	1
DC3000/delta hrp 24h	0.99236	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85066	0.124
DC3000 delta B/DC3000 delta AB	0.72046	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84295	1
Exp 36h	1.14817	1
Exp 60h	0.61794	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.001	1
Var 0h	1.64275	0.782
Var 12h I row2-row1	0.87765	0.514
Var 12h NI row2-row1	1.07301	1
Var 36h I row2-row1	1.1388	0.908
Var 36h NI row2-row1	1.04397	1
Var 60h I row2-row1	0.94417	0.952
Var 60h NI row2-row1	0.9849	1
Time course 0hI-0hNI	0.99154	1
Time course 12hI-12hNI	1.04248	0.724
Time course 36hI-36hNI	1.36677	0.006
Time course 60hI-60hNI	1.85349	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)	1.03791	0.863
transgenic ySAMdc/azygous control (breaker)	0.64511	0.139
transgenic ySAMdc/azygous control (red)	1.50658	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03296	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78566	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16344	0.14
Manapal/WT (break)	0.84705	1
Manapal/WT (red)	1.55174	0.413