Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00127	0.975
27DAP/17DAP	1.19507	0.8
39DAP/27DAP	0.85661	0.474
41DAP/39DAP	1.03814	0.814
42DAP/41DAP	1.20787	0.852
43DAP/42DAP	1.0669	1
47DAP/43DAP	1.03454	1
52DAP/47DAP	0.87387	0.618
57DAP/52DAP	0.94212	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09691	0.068
17DAP/reference	1.0437	0.457
27DAP/reference	1.03138	0.794
39DAP/reference	0.98794	0.874
41DAP/reference	1.06058	0.043
42DAP/reference	0.99886	0.688
43DAP/reference	1.0349	0.518
47DAP/reference	0.9569	0.127
52DAP/reference	1.02909	0.951
57DAP/reference	1.05824	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99573	0.847
27DAP/17DAP	1.03874	0.863
39DAP/27DAP	0.98885	0.932
41DAP/39DAP	0.99182	1
42DAP/41DAP	0.97264	0.712
43DAP/42DAP	1.00567	1
47DAP/43DAP	0.96585	0.743
52DAP/47DAP	0.98946	0.93
57DAP/52DAP	1.03231	0.8
57DAP/7DAP	1.01338	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64251	0.086
17DAP/reference	0.60054	0.013
27DAP/reference	0.63909	0.01
39DAP/reference	0.62958	0.011
41DAP/reference	0.68703	0.016
42DAP/reference	0.59875	0.01
43DAP/reference	0.59726	0.017
47DAP/reference	0.77452	0.168
52DAP/reference	0.53118	0.012
57DAP/reference	0.44598	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9967	0.907
17DAP/reference	0.98728	0.659
27DAP/reference	0.89865	0.09
39DAP/reference	0.89446	0.053
41DAP/reference	0.9471	0.226
42DAP/reference	1.01095	1
43DAP/reference	0.75574	0.108
47DAP/reference	1.11739	0.056
52DAP/reference	0.97551	0.239
57DAP/reference	1.01927	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31422	0.109
17DAP/reference	0.82558	0.217
27DAP/reference	0.76399	0.053
39DAP/reference	0.77975	0.017
41DAP/reference	0.54226	0.018
42DAP/reference	0.5611	0.016
43DAP/reference	0.65749	0.027
47DAP/reference	1.02689	0.82
52DAP/reference	0.9521	0.562
57DAP/reference	0.81493	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09117	0.916
26DAP/20DAP	1.03088	0.962
34DAP/26DAP	1.06171	0.819
51DAP/34DAP	1.03331	0.719
52DAP/51DAP	0.99841	1
53DAP/52DAP	0.99767	0.998
55DAP/53DAP	0.989	0.852
57DAP/55DAP	1.02688	0.927
62DAP/57DAP	0.95714	0.681
68DAP/62DAP	0.8731	0.609
68DAP/14DAP	1.24579	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03361	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78486	0.351
Mature Green Tomato/Ripe Tomato	0.7045	0.042
Immature Eggplant/Mature Eggplant	0.67096	0.134
Ripe Pepper/Ripe Tomato	0.40442	0.224
Mature Eggplant/Ripe Tomato	0.42719	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97854	0.961
1-1-2/M82	0.95336	0.958
12-2/M82	0.97743	0.955
12-4/M82	0.94384	1
1-3/M82	1.05964	1
2-1-1/M82	1.10156	1
2-1/M82	1.0211	1
2-6/M82	0.93917	1
3-2/M82	1.03525	0.967
4-1-1/M82	0.98965	1
4-1/M82	0.97481	1
4-3-2/M82	0.90942	1
4-3/M82	0.97591	1
5-3/M82	1.00993	1
6-2/M82	1.08248	1
6-3/M82	1.02083	1
7-1/M82	1.20414	1
7-2/M82	0.96159	1
9-3-2/M82	0.85284	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21827	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.76421	0.298
IL12-4/WTpooled	0.72049	0.71
IL1-4/WTpooled	0.90531	0.834
WT/WTpooled	0.94358	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	0.93842	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97826	1
DC3000/delta hrp 6h	0.93888	0.95
DC3000/delta hrp 12h	0.93419	1
DC3000/delta hrp 24h	1.33547	0.082

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03346	0.27
DC3000 delta B/DC3000 delta AB	1.04622	0.51

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.36913	0.254
Exp 36h	1.16591	0.693
Exp 60h	1.44988	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04528	1
Var 0h	0.63129	1
Var 12h I row2-row1	1.08239	0.228
Var 12h NI row2-row1	0.96501	0.906
Var 36h I row2-row1	1.1141	1
Var 36h NI row2-row1	0.97377	0.791
Var 60h I row2-row1	1.04938	0.543
Var 60h NI row2-row1	1.19589	0.904
Time course 0hI-0hNI	1.10395	0.764
Time course 12hI-12hNI	1.00551	0.892
Time course 36hI-36hNI	1.04492	0.722
Time course 60hI-60hNI	1.21945	0.019

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)	0.95472	0.662
transgenic ySAMdc/azygous control (breaker)	0.7043	0.139
transgenic ySAMdc/azygous control (red)	1.21271	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97787	0.214

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.57909	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9326	1
Manapal/WT (break)	0.83857	1
Manapal/WT (red)	0.64219	0.181