Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.2.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01273	0.876
27DAP/17DAP	0.87862	0.7
39DAP/27DAP	0.79748	0.414
41DAP/39DAP	1.06863	0.992
42DAP/41DAP	1.22532	0.871
43DAP/42DAP	1.09223	0.945
47DAP/43DAP	1.19112	0.715
52DAP/47DAP	0.83271	0.609
57DAP/52DAP	1.4543	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9376	0.352
17DAP/reference	0.91016	0.169
27DAP/reference	0.98015	0.668
39DAP/reference	0.95041	0.446
41DAP/reference	0.77873	0.049
42DAP/reference	0.95838	0.151
43DAP/reference	0.99384	0.84
47DAP/reference	1.05977	0.817
52DAP/reference	1.2344	0.256
57DAP/reference	1.09571	0.291

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0976	0.326
27DAP/17DAP	0.99798	0.943
39DAP/27DAP	1.06294	0.845
41DAP/39DAP	0.90555	0.398
42DAP/41DAP	1.05744	0.947
43DAP/42DAP	1.08176	0.585
47DAP/43DAP	1.05433	0.699
52DAP/47DAP	1.04805	0.823
57DAP/52DAP	0.84579	0.501
57DAP/7DAP	0.86903	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02465	1
17DAP/reference	1.33777	0.059
27DAP/reference	1.41806	0.012
39DAP/reference	1.04002	1
41DAP/reference	1.44802	0.072
42DAP/reference	1.14218	0.686
43DAP/reference	1.33603	0.028
47DAP/reference	1.06276	0.717
52DAP/reference	1.518	0.016
57DAP/reference	1.43963	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89261	0.157
17DAP/reference	0.86053	0.021
27DAP/reference	0.92667	0.317
39DAP/reference	0.89212	0.159
41DAP/reference	1.04398	1
42DAP/reference	0.94393	0.355
43DAP/reference	0.95967	0.486
47DAP/reference	0.72969	0.021
52DAP/reference	0.97961	0.469
57DAP/reference	0.86329	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08464	0.616
17DAP/reference	0.97784	0.658
27DAP/reference	1.42602	0.028
39DAP/reference	1.26517	0.043
41DAP/reference	1.4575	0.044
42DAP/reference	1.12047	0.529
43DAP/reference	1.12239	0.79
47DAP/reference	0.92627	0.383
52DAP/reference	1.2544	0.473
57DAP/reference	0.97346	0.543

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14073	0.966
26DAP/20DAP	1.15201	0.941
34DAP/26DAP	0.89527	0.702
51DAP/34DAP	1.37766	0.785
52DAP/51DAP	1.01766	1
53DAP/52DAP	0.77755	0.393
55DAP/53DAP	0.85189	0.163
57DAP/55DAP	0.58855	0.1
62DAP/57DAP	0.79898	0.016
68DAP/62DAP	1.33217	0.472
68DAP/14DAP	1.20273	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.78288	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69072	0.194
Mature Green Tomato/Ripe Tomato	0.96155	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.0068	1
Mature Eggplant/Ripe Tomato	0.51458	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20199
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.76765	0.319
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.89039
4-3/M82	N/A	N/A
5-3/M82	1.03297	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.10172
7-2/M82	N/A	N/A
9-3-2/M82	1.10347

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95195	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97215
IL12-4/WTpooled	1.04451	0.737
IL1-4/WTpooled	1.10034
WT/WTpooled	0.865	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	1.05852	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21464	0.774
DC3000/delta hrp 6h	0.907	0.95
DC3000/delta hrp 12h	1.19377	1
DC3000/delta hrp 24h	1.24529	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95198	1
Exp 36h	0.83862	0.504
Exp 60h	0.75683	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9724	1
Var 0h	1.07918	0.98
Var 12h I row2-row1	0.97035	0.705
Var 12h NI row2-row1	0.98039	0.906
Var 36h I row2-row1	0.98895	1
Var 36h NI row2-row1	1.03664	1
Var 60h I row2-row1	0.78504	0.439
Var 60h NI row2-row1	0.78629	0.977
Time course 0hI-0hNI	0.93983	0.679
Time course 12hI-12hNI	0.99339	1
Time course 36hI-36hNI	1.02715	0.799
Time course 60hI-60hNI	0.87675	0.081

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)	1.05004	0.339
transgenic ySAMdc/azygous control (breaker)	0.96722	1
transgenic ySAMdc/azygous control (red)	0.87863	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03425	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.53312	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70615	0.172
Manapal/WT (break)	0.94018	1
Manapal/WT (red)	1.08286	1