Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.15.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00112	0.927
27DAP/17DAP	1.12286	0.868
39DAP/27DAP	0.85621	0.458
41DAP/39DAP	1.22197	0.649
42DAP/41DAP	1.0757	1
43DAP/42DAP	0.87789	0.743
47DAP/43DAP	1.03746	0.856
52DAP/47DAP	1.05945	0.949
57DAP/52DAP	1.07048	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92962	0.077
17DAP/reference	0.95591	0.298
27DAP/reference	0.98641	0.668
39DAP/reference	0.99239	0.901
41DAP/reference	0.97219	0.434
42DAP/reference	0.97225	0.12
43DAP/reference	1.03016	0.445
47DAP/reference	0.94543	0.098
52DAP/reference	0.98573	0.564
57DAP/reference	0.99316	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96313	0.644
27DAP/17DAP	0.99195	0.969
39DAP/27DAP	1.0072	0.874
41DAP/39DAP	0.9999	1
42DAP/41DAP	0.93521	0.447
43DAP/42DAP	0.98896	0.831
47DAP/43DAP	1.01219	0.95
52DAP/47DAP	1.01635	0.956
57DAP/52DAP	0.98202	0.695
57DAP/7DAP	1.01888	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89785	0.039
17DAP/reference	0.98391	0.447
27DAP/reference	0.98322	0.494
39DAP/reference	1.03842	0.237
41DAP/reference	0.95928	0.166
42DAP/reference	1.03733	0.889
43DAP/reference	0.97736	0.403
47DAP/reference	0.97889	0.504
52DAP/reference	1.01524	0.886
57DAP/reference	0.95161	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01196	0.885
17DAP/reference	0.9687	0.41
27DAP/reference	0.9189	0.173
39DAP/reference	0.88839	0.029
41DAP/reference	0.90131	0.081
42DAP/reference	0.95102	0.189
43DAP/reference	0.99989	0.875
47DAP/reference	0.98393	0.359
52DAP/reference	0.95454	0.171
57DAP/reference	0.99717	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94681	0.065
17DAP/reference	0.97365	0.433
27DAP/reference	1.05847	0.137
39DAP/reference	1.06137	0.108
41DAP/reference	0.98614	0.56
42DAP/reference	0.93346	0.028
43DAP/reference	0.94479	0.206
47DAP/reference	0.90881	0.069
52DAP/reference	0.99714	0.888
57DAP/reference	0.76577	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99868	1
26DAP/20DAP	0.8968	0.512
34DAP/26DAP	0.96588	0.927
51DAP/34DAP	1.13497	0.402
52DAP/51DAP	1.08848	0.367
53DAP/52DAP	1.06624	0.91
55DAP/53DAP	0.9617	0.746
57DAP/55DAP	1.17115	0.728
62DAP/57DAP	1.08532	0.935
68DAP/62DAP	1.01565	1
68DAP/14DAP	0.90219	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94486	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85028	0.458
Mature Green Tomato/Ripe Tomato	0.86018	0.051
Immature Eggplant/Mature Eggplant	1.7389	0.076
Ripe Pepper/Ripe Tomato	1.26759	1
Mature Eggplant/Ripe Tomato	0.88039	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11076	0.877
1-1-2/M82	0.98607	1
12-2/M82	1.07757
12-4/M82	0.97027	1
1-3/M82	0.90805	0.501
2-1-1/M82	0.89187
2-1/M82	N/A	N/A
2-6/M82	0.98056	1
3-2/M82	N/A	N/A
4-1-1/M82	1.04469	1
4-1/M82	0.99557	1
4-3-2/M82	0.77532	1
4-3/M82	1.06272	1
5-3/M82	1.06578	1
6-2/M82	0.94989	1
6-3/M82	0.98485	1
7-1/M82	N/A	N/A
7-2/M82	0.99234	1
9-3-2/M82	0.80927	0.449

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	0.73674	0.699
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	1.10872	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.9338	0.95
DC3000/delta hrp 12h	0.9672	1
DC3000/delta hrp 24h	1.11364	0.502

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	1.23939	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07814	1
Exp 36h	N/A	N/A
Exp 60h	1.06682	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97016	1
Var 0h	1.03282	1
Var 12h I row2-row1	1.25238	0.324
Var 12h NI row2-row1	1.10761	1
Var 36h I row2-row1	0.93953	1
Var 36h NI row2-row1	0.90606	0.706
Var 60h I row2-row1	1.23125	1
Var 60h NI row2-row1	1.25087	0.904
Time course 0hI-0hNI	1.04461	0.852
Time course 12hI-12hNI	1.05514	0.724
Time course 36hI-36hNI	1.03637	0.453
Time course 60hI-60hNI	1.32198	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)	1.00345	1
transgenic ySAMdc/azygous control (breaker)	0.9052	0.15
transgenic ySAMdc/azygous control (red)	1.03338	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0189	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10975	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93462	1
Manapal/WT (break)	0.74036	0.333
Manapal/WT (red)	0.83389	0.199