Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11584	0.83
27DAP/17DAP	1.00072	1
39DAP/27DAP	1.10281	0.972
41DAP/39DAP	1.09675	0.649
42DAP/41DAP	3.20784	0.066
43DAP/42DAP	1.14662	0.968
47DAP/43DAP	1.74825	0.469
52DAP/47DAP	0.70061	0.282
57DAP/52DAP	1.33229	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86774	0.224
17DAP/reference	0.36472
27DAP/reference	0.50488	0.075
39DAP/reference	0.74281
41DAP/reference	N/A	N/A
42DAP/reference	2.68818	0.103
43DAP/reference	1.9722	0.445
47DAP/reference	2.9505	0.001
52DAP/reference	2.29837	0.041
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08742	0.719
27DAP/17DAP	0.6747	0.047
39DAP/27DAP	0.86953	0.496
41DAP/39DAP	0.69613	0.209
42DAP/41DAP	1.56909	0.111
43DAP/42DAP	1.97766	0.015
47DAP/43DAP	0.9634	0.833
52DAP/47DAP	0.99523	0.951
57DAP/52DAP	0.91229	0.507
57DAP/7DAP	1.23094	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22626	0.452
17DAP/reference	0.59606	0.014
27DAP/reference	0.52669	0.01
39DAP/reference	0.27081	0.011
41DAP/reference	0.27337	0.011
42DAP/reference	0.32627	0.01
43DAP/reference	0.3073	0.009
47DAP/reference	1.2156	0.671
52DAP/reference	0.23025	0.009
57DAP/reference	0.49326	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8086	0.145
17DAP/reference	0.67227	0.006
27DAP/reference	0.80604	0.081
39DAP/reference	0.74067	0.045
41DAP/reference	0.68083	0.006
42DAP/reference	0.89399	0.098
43DAP/reference	0.50801	0.003
47DAP/reference	0.94806	0.368
52DAP/reference	0.40561	0.003
57DAP/reference	0.60415	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.4355	0.058
17DAP/reference	0.95462	0.519
27DAP/reference	1.14055	0.695
39DAP/reference	0.61313	0.009
41DAP/reference	0.50698	0.019
42DAP/reference	1.16888	0.361
43DAP/reference	2.23693	0.767
47DAP/reference	2.63366	0.005
52DAP/reference	1.11506	0.385
57DAP/reference	2.40064	0.046

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07434	1
26DAP/20DAP	1.26232	0.308
34DAP/26DAP	1.33728	0.304
51DAP/34DAP	0.88707	0.449
52DAP/51DAP	1.25475	0.689
53DAP/52DAP	1.22287	0.688
55DAP/53DAP	0.75225	0.039
57DAP/55DAP	1.56893	0.805
62DAP/57DAP	0.70189	0.003
68DAP/62DAP	1.0337	0.939
68DAP/14DAP	1.3113	0.05

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3528	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09286	0.176
Mature Green Tomato/Ripe Tomato	0.17474	0.017
Immature Eggplant/Mature Eggplant	1.03805	0.278
Ripe Pepper/Ripe Tomato	0.35368	0.293
Mature Eggplant/Ripe Tomato	0.79428	1

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	0.72768
12-4/M82	N/A	N/A
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	0.97162
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	1.03198
IL2-6/WTpooled	1.09254	0.659
IL7-5/WTpooled	0.866
IL7-3/WTpooled	0.99613	1
IL12-4/WTpooled	1.17507	0.891
IL1-4/WTpooled	0.97192	1
WT/WTpooled	1.088	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	1.00712	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98693	1
DC3000/delta hrp 6h	0.98025	0.95
DC3000/delta hrp 12h	1.16759	1
DC3000/delta hrp 24h	0.76956	0.076

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66548	0.232
DC3000 delta B/DC3000 delta AB	0.98429

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02281	1
Exp 36h	1.00424	1
Exp 60h	1.00593	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95887
Var 0h	0.76524	0.457
Var 12h I row2-row1	0.93139	0.363
Var 12h NI row2-row1	0.98643	1
Var 36h I row2-row1	1.32571	0.41
Var 36h NI row2-row1	0.58797	0.482
Var 60h I row2-row1	0.8538	0.306
Var 60h NI row2-row1	0.92465	0.977
Time course 0hI-0hNI	1.00937	1
Time course 12hI-12hNI	0.92766	0.446
Time course 36hI-36hNI	1.28266	0.035
Time course 60hI-60hNI	1.22611	0.115

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)	0.78969	0.286
transgenic ySAMdc/azygous control (breaker)	1.11954	1
transgenic ySAMdc/azygous control (red)	0.86528	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11461	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05729	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94609	1
Manapal/WT (break)	1.41241	0.123
Manapal/WT (red)	0.7637	0.315