Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.11.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92872	0.586
27DAP/17DAP	1.03825	0.902
39DAP/27DAP	1.05718	0.84
41DAP/39DAP	1.06016	0.722
42DAP/41DAP	1.07908	0.843
43DAP/42DAP	1.26284	0.698
47DAP/43DAP	1.03509	1
52DAP/47DAP	1.02453	0.976
57DAP/52DAP	1.01062	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15692	0.121
17DAP/reference	1.48855	0.21
27DAP/reference	1.38934	0.051
39DAP/reference	1.22931	0.117
41DAP/reference	1.48908	0.009
42DAP/reference	1.17661	0.137
43DAP/reference	1.00635	0.924
47DAP/reference	1.31189	0.026
52DAP/reference	1.13624	0.453
57DAP/reference	1.11927	0.153

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94898	0.595
27DAP/17DAP	1.09425	0.788
39DAP/27DAP	1.3576	0.054
41DAP/39DAP	0.96669	0.945
42DAP/41DAP	1.22925	0.343
43DAP/42DAP	0.63498	0.022
47DAP/43DAP	0.93706	0.457
52DAP/47DAP	0.83924	0.585
57DAP/52DAP	1.01828	0.869
57DAP/7DAP	1.58626

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74117	0.066
17DAP/reference	1.01535	1
27DAP/reference	1.01104	0.974
39DAP/reference	0.71128	0.011
41DAP/reference	0.92154	0.16
42DAP/reference	0.85353	0.09
43DAP/reference	0.85503	0.047
47DAP/reference	0.93909	0.383
52DAP/reference	0.78513	0.02
57DAP/reference	0.91769	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92579	0.639
17DAP/reference	1.19043	0.176
27DAP/reference	1.18404	0.271
39DAP/reference	1.48922	0.013
41DAP/reference	1.13678	0.614
42DAP/reference	1.0786	0.744
43DAP/reference	1.22512	0.386
47DAP/reference	1.11293	0.498
52DAP/reference	0.86561	0.259
57DAP/reference	1.03426	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05535	0.659
17DAP/reference	1.05102	0.675
27DAP/reference	0.92414	0.337
39DAP/reference	1.04451	1
41DAP/reference	1.08486	0.239
42DAP/reference	1.10327	0.382
43DAP/reference	1.15369	0.499
47DAP/reference	1.07252	0.934
52DAP/reference	1.25543	0.155
57DAP/reference	1.37641	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.70562
26DAP/20DAP	0.90591	1
34DAP/26DAP	0.99697	1
51DAP/34DAP	1.16996	0.511
52DAP/51DAP	1.02067	0.939
53DAP/52DAP	0.89768	0.587
55DAP/53DAP	0.97235	0.807
57DAP/55DAP	1.04807	0.821
62DAP/57DAP	1.08634	0.902
68DAP/62DAP	1.56524	0.792
68DAP/14DAP	0.83137	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19642	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.48118	0.814
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.79104	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95814	0.907
1-1-2/M82	0.98029	1
12-2/M82	0.98574
12-4/M82	1.11742
1-3/M82	0.71565	0.378
2-1-1/M82	1.01546
2-1/M82	N/A	N/A
2-6/M82	1.09765	1
3-2/M82	1.14064
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	0.78473
5-3/M82	0.94193	1
6-2/M82	N/A	N/A
6-3/M82	1.44884
7-1/M82	0.9565
7-2/M82	1.01991	0.282
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8958	0.247
IL2-6/WTpooled	0.83391	0.348
IL7-5/WTpooled	1.24497	0.792
IL7-3/WTpooled	0.96085	1
IL12-4/WTpooled	1.09792	0.891
IL1-4/WTpooled	1.05621	1
WT/WTpooled	0.89932	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	0.90178	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99343	1
DC3000/delta hrp 6h	0.4652
DC3000/delta hrp 12h	0.90874	1
DC3000/delta hrp 24h	0.80621	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84963	0.629
DC3000 delta B/DC3000 delta AB	1.14266	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12963	1
Exp 36h	1.17528	1
Exp 60h	0.93257	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93657	1
Var 0h	0.81198	0.933
Var 12h I row2-row1	1.14811	0.263
Var 12h NI row2-row1	1.20117	0.34
Var 36h I row2-row1	0.80892	1
Var 36h NI row2-row1	0.95286	0.791
Var 60h I row2-row1	0.75819	0.306
Var 60h NI row2-row1	0.88501	0.866
Time course 0hI-0hNI	1.04506	0.764
Time course 12hI-12hNI	1.02079	0.788
Time course 36hI-36hNI	1.00172	0.811
Time course 60hI-60hNI	1.11347	0.137

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)	1.09319	0.612
transgenic ySAMdc/azygous control (breaker)	0.78844	0.49
transgenic ySAMdc/azygous control (red)	1.09039	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.32262	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02941	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84312	1
Manapal/WT (break)	1.09294	1
Manapal/WT (red)	1.09447	0.413