Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.10.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93426	0.033
27DAP/17DAP	1.18364	0.845
39DAP/27DAP	0.94269	0.663
41DAP/39DAP	0.58433	0.041
42DAP/41DAP	0.69586	0.397
43DAP/42DAP	1.05074	1
47DAP/43DAP	0.86504	0.565
52DAP/47DAP	1.02408	0.991
57DAP/52DAP	0.76709	0.39

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00588	1
17DAP/reference	1.06829	0.064
27DAP/reference	1.00131	0.923
39DAP/reference	1.03638	0.286
41DAP/reference	1.06625	0.085
42DAP/reference	0.90948	0.056
43DAP/reference	1.05031	0.36
47DAP/reference	0.93021	0.013
52DAP/reference	0.87773	0.131
57DAP/reference	0.83964	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01855	0.871
27DAP/17DAP	0.88877	0.121
39DAP/27DAP	0.87587	0.089
41DAP/39DAP	1.08056	0.837
42DAP/41DAP	1.09159	0.663
43DAP/42DAP	0.92486	0.206
47DAP/43DAP	0.79018	0.128
52DAP/47DAP	1.88848	0.17
57DAP/52DAP	2.19633	0.036
57DAP/7DAP	0.31362	0.143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06966	0.444
17DAP/reference	1.0705	0.134
27DAP/reference	1.11227	0.007
39DAP/reference	1.05916	0.282
41DAP/reference	1.17089	0.06
42DAP/reference	1.1156
43DAP/reference	1.1477	0.344
47DAP/reference	1.06939	0.632
52DAP/reference	1.16312	0.212
57DAP/reference	1.17661	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02428	0.732
17DAP/reference	1.00548	0.941
27DAP/reference	0.8721	0.15
39DAP/reference	1.10561	0.073
41DAP/reference	1.13914	0.502
42DAP/reference	0.87186	0.121
43DAP/reference	1.0854	0.251
47DAP/reference	0.93457	0.094
52DAP/reference	1.08088	0.02
57DAP/reference	1.12859	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04928	0.588
17DAP/reference	1.04781	0.712
27DAP/reference	1.42455	0.039
39DAP/reference	1.35809	0.067
41DAP/reference	1.162	0.174
42DAP/reference	1.03145	1
43DAP/reference	0.91549	0.416
47DAP/reference	0.97504	0.509
52DAP/reference	1.05668	0.714
57DAP/reference	0.56143	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05346	0.966
26DAP/20DAP	3.20525	0.477
34DAP/26DAP	4.36159	1
51DAP/34DAP	1.29064	0.779
52DAP/51DAP	6.47934	0.033
53DAP/52DAP	0.69687	0.119
55DAP/53DAP	1.63387	0.031
57DAP/55DAP	0.36568	0.019
62DAP/57DAP	1.93677	0.35
68DAP/62DAP	1.58725	0.931
68DAP/14DAP	1.07208	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.3536	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	8.12993	0.015
Immature Eggplant/Mature Eggplant	1.12007	0.15
Ripe Pepper/Ripe Tomato	0.29313	0.224
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80895
1-1-2/M82	1.14041
12-2/M82	N/A	N/A
12-4/M82	0.78305
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	0.9966
4-1-1/M82	N/A	N/A
4-1/M82	1.28627
4-3-2/M82	0.86845
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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.94734

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93802	1
IL2-6/WTpooled	1.17412	0.395
IL7-5/WTpooled	1.08161	0.792
IL7-3/WTpooled	0.76822	0.293
IL12-4/WTpooled	1.00471	1
IL1-4/WTpooled	0.98906	0.834
WT/WTpooled	0.93483	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	0.94704	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12782	0.921
DC3000/delta hrp 6h	1.09049	1
DC3000/delta hrp 12h	1.15937	1
DC3000/delta hrp 24h	1.21058	0.058

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12868	0.094
DC3000 delta B/DC3000 delta AB	1.37551	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04375	1
Exp 36h	1.35536	0.693
Exp 60h	1.19741	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01746	1
Var 0h	0.93325	1
Var 12h I row2-row1	0.8599	0.338
Var 12h NI row2-row1	1.02566	1
Var 36h I row2-row1	0.86858	1
Var 36h NI row2-row1	1.36968	0.276
Var 60h I row2-row1	0.99831	1
Var 60h NI row2-row1	0.97252	1
Time course 0hI-0hNI	0.96685	0.839
Time course 12hI-12hNI	1.0312	0.827
Time course 36hI-36hNI	1.01637	0.753
Time course 60hI-60hNI	0.77816	0.007

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)	0.94233	0.338
transgenic ySAMdc/azygous control (breaker)	1.00135	1
transgenic ySAMdc/azygous control (red)	0.88925	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97107	0.227

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9024	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89659	1
Manapal/WT (break)	0.96232	1
Manapal/WT (red)	1.15525	1