Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79523	0.051
27DAP/17DAP	1.23778	0.833
39DAP/27DAP	1.23358	0.35
41DAP/39DAP	0.77948	0.299
42DAP/41DAP	0.88199	1
43DAP/42DAP	0.93564	0.877
47DAP/43DAP	1.00256	0.913
52DAP/47DAP	1.63304	0.294
57DAP/52DAP	1.00734	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01618	1
17DAP/reference	0.8796	0.02
27DAP/reference	1.0841	0.696
39DAP/reference	0.79756	0.164
41DAP/reference	0.71364	0.008
42DAP/reference	1.23106	0.219
43DAP/reference	N/A	N/A
47DAP/reference	0.97232	0.535
52DAP/reference	1.09419	0.84
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90783	0.363
27DAP/17DAP	1.10592	0.587
39DAP/27DAP	0.94686	0.579
41DAP/39DAP	1.14123	0.455
42DAP/41DAP	0.87952	0.113
43DAP/42DAP	0.91005	0.216
47DAP/43DAP	0.98749	0.933
52DAP/47DAP	1.02109	0.945
57DAP/52DAP	1.90412	0.034
57DAP/7DAP	1.23839	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08988	0.444
17DAP/reference	1.15072	0.477
27DAP/reference	1.15818	0.131
39DAP/reference	1.10047	0.511
41DAP/reference	1.45171	0.018
42DAP/reference	1.29271	0.233
43DAP/reference	0.97075	0.502
47DAP/reference	1.17332	0.224
52DAP/reference	1.32287	0.113
57DAP/reference	0.95174	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87388	0.204
17DAP/reference	0.87257	0.189
27DAP/reference	0.91117	0.327
39DAP/reference	1.008	0.586
41DAP/reference	1.25846	0.047
42DAP/reference	1.02708	0.759
43DAP/reference	0.83805	0.17
47DAP/reference	1.14327	0.291
52DAP/reference	0.87052	0.006
57DAP/reference	0.98043	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48514	0.064
17DAP/reference	1.01744	0.87
27DAP/reference	1.09234	0.695
39DAP/reference	0.95128	0.43
41DAP/reference	1.17357	0.296
42DAP/reference	1.63594	0.035
43DAP/reference	1.52328	0.04
47DAP/reference	0.96904	0.494
52DAP/reference	1.15397	0.517
57DAP/reference	1.33841	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03028	1
26DAP/20DAP	0.97104	1
34DAP/26DAP	0.91859	0.763
51DAP/34DAP	1.54126	0.045
52DAP/51DAP	0.6918	0.151
53DAP/52DAP	3.67305	0.026
55DAP/53DAP	0.65214	0.031
57DAP/55DAP	0.7341	0.159
62DAP/57DAP	0.47142	0.088
68DAP/62DAP	1.30572	0.767
68DAP/14DAP	1.00569	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97375	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26083	0.058
Mature Green Tomato/Ripe Tomato	0.74654	0.132
Immature Eggplant/Mature Eggplant	1.17315	0.101
Ripe Pepper/Ripe Tomato	0.75781	0.293
Mature Eggplant/Ripe Tomato	0.61262	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.40499	N/A
1-1-2/M82	0.93219	0.804
12-2/M82	0.90452	0.623
12-4/M82	1.06252	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.06313	N/A
2-1/M82	N/A	N/A
2-6/M82	1.10889	N/A
3-2/M82	N/A	N/A
4-1-1/M82	1.23703	N/A
4-1/M82	0.88021	N/A
4-3-2/M82	0.97592	N/A
4-3/M82	1.0966	N/A
5-3/M82	1.28076	0.572
6-2/M82	1.43963	N/A
6-3/M82	0.73432	N/A
7-1/M82	0.96769	N/A
7-2/M82	1.25832	0.282
9-3-2/M82	0.957	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78588	1
IL2-6/WTpooled	0.93401	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93073	1
IL12-4/WTpooled	1.22481	0.673
IL1-4/WTpooled	0.8612	0.699
WT/WTpooled	1.0268	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	0.7645	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88246	0.839
DC3000/delta hrp 6h	1.26178	1
DC3000/delta hrp 12h	1.06551	1
DC3000/delta hrp 24h	0.98779	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12939	1
DC3000 delta B/DC3000 delta AB	1.13698	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04883	1
Exp 36h	1.09541	1
Exp 60h	1.14202	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95123	1
Var 0h	0.96194	1
Var 12h I row2-row1	0.96723	0.627
Var 12h NI row2-row1	1.01902	1
Var 36h I row2-row1	1.1551	0.41
Var 36h NI row2-row1	1.22155	0.482
Var 60h I row2-row1	0.76498	0.293
Var 60h NI row2-row1	1.35436	0.793
Time course 0hI-0hNI	0.98273	0.947
Time course 12hI-12hNI	0.95676	0.682
Time course 36hI-36hNI	0.84886	0.053
Time course 60hI-60hNI	1.02075	1

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)	0.92497	0.33
transgenic ySAMdc/azygous control (breaker)	0.91744	0.49
transgenic ySAMdc/azygous control (red)	1.19673	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.15807	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26922	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94486	1
Manapal/WT (break)	0.72938	0.333
Manapal/WT (red)	0.90744	0.315