Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.7.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1498	1
27DAP/17DAP	0.75335	0.277
39DAP/27DAP	1.07385	1
41DAP/39DAP	0.66907	0.09
42DAP/41DAP	1.30946	0.802
43DAP/42DAP	1.2632	0.676
47DAP/43DAP	1.19721	0.668
52DAP/47DAP	0.89932	0.693
57DAP/52DAP	1.07865	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91525	0.344
17DAP/reference	0.96935	0.597
27DAP/reference	0.9674	0.567
39DAP/reference	0.9205	0.206
41DAP/reference	0.8917	0.154
42DAP/reference	0.91759	0.05
43DAP/reference	0.99489	0.861
47DAP/reference	0.89172	0.018
52DAP/reference	0.92366	0.283
57DAP/reference	0.90539	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.785	0.093
27DAP/17DAP	1.29011	0.381
39DAP/27DAP	0.74464	0.036
41DAP/39DAP	1.12696	0.876
42DAP/41DAP	1.01331	0.926
43DAP/42DAP	1.12166	0.478
47DAP/43DAP	1.02759	0.934
52DAP/47DAP	1.21323	0.422
57DAP/52DAP	1.17837	0.33
57DAP/7DAP	0.78684	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93045	0.402
17DAP/reference	1.11338	0.477
27DAP/reference	1.20239	0.246
39DAP/reference	0.96853	0.474
41DAP/reference	1.06423	0.791
42DAP/reference	0.88785	0.2
43DAP/reference	1.12547	0.083
47DAP/reference	0.85209	0.079
52DAP/reference	0.83233	0.066
57DAP/reference	0.82309	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1433	0.238
17DAP/reference	0.91972	0.245
27DAP/reference	0.97349	0.483
39DAP/reference	1.00468	0.586
41DAP/reference	0.90949	0.121
42DAP/reference	0.85241	0.089
43DAP/reference	1.07717	0.662
47DAP/reference	0.80531	0.058
52DAP/reference	0.90339	0.086
57DAP/reference	1.10377	0.672

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98515	0.607
17DAP/reference	0.91287	0.328
27DAP/reference	0.9082	0.165
39DAP/reference	1.00155	0.755
41DAP/reference	0.99746	0.682
42DAP/reference	1.18908	0.45
43DAP/reference	0.9532	0.449
47DAP/reference	0.82746	0.045
52DAP/reference	1.01658	0.854
57DAP/reference	1.06361	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45555	0.966
26DAP/20DAP	0.84383	0.512
34DAP/26DAP	1.00154	1
51DAP/34DAP	1.04437	0.795
52DAP/51DAP	0.9397	1
53DAP/52DAP	0.79024	0.194
55DAP/53DAP	1.15434	0.904
57DAP/55DAP	0.81088	0.351
62DAP/57DAP	1.08643	0.002
68DAP/62DAP	0.76837	0.747
68DAP/14DAP	1.37239	0.146

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62206	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.29731
Immature Eggplant/Mature Eggplant	7.85354	0.049
Ripe Pepper/Ripe Tomato	0.43617	1
Mature Eggplant/Ripe Tomato	5.20906

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.30785
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.85408
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.64165
IL2-6/WTpooled	1.08983	0.584
IL7-5/WTpooled	0.82842	1
IL7-3/WTpooled	0.53998	0.31
IL12-4/WTpooled	1.08052	0.891
IL1-4/WTpooled	1.02285	1
WT/WTpooled	0.91299	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	0.98591	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98885	1
DC3000/delta hrp 6h	1.22633	0.857
DC3000/delta hrp 12h	1.0516	1
DC3000/delta hrp 24h	0.56656	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.36494	0.025
DC3000 delta B/DC3000 delta AB	0.31737	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86786	1
Exp 36h	0.64493	0.426
Exp 60h	0.47201	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02359	1
Var 0h	0.86919	1
Var 12h I row2-row1	0.85994	0.357
Var 12h NI row2-row1	0.57935	0.33
Var 36h I row2-row1	0.75244	0.575
Var 36h NI row2-row1	1.71189	1
Var 60h I row2-row1	1.50879	0.543
Var 60h NI row2-row1	1.40644	0.904
Time course 0hI-0hNI	0.73025	0.045
Time course 12hI-12hNI	1.03472	0.867
Time course 36hI-36hNI	0.91382	0.187
Time course 60hI-60hNI	0.083	0.005

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)	1.0353	0.571
transgenic ySAMdc/azygous control (breaker)	1.24024	0.162
transgenic ySAMdc/azygous control (red)	0.99916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75198	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.87428	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.01444	0.086
Manapal/WT (break)	1.63072	0.13
Manapal/WT (red)	N/A	N/A