Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6608	0.054
27DAP/17DAP	0.84129	0.585
39DAP/27DAP	0.97712	0.719
41DAP/39DAP	1.03805	0.868
42DAP/41DAP	0.91291	1
43DAP/42DAP	1.12526	1
47DAP/43DAP	0.8661	0.568
52DAP/47DAP	1.12575	0.898
57DAP/52DAP	0.69084	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96039	0.489
17DAP/reference	0.65971	0.01
27DAP/reference	1.05982	0.909
39DAP/reference	0.70004	0.014
41DAP/reference	0.6905	0.021
42DAP/reference	1.03225	0.628
43DAP/reference	0.937	0.316
47DAP/reference	0.99146	0.418
52DAP/reference	1.66586	0.026
57DAP/reference	1.41796	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72532	0.057
27DAP/17DAP	1.66571	0.079
39DAP/27DAP	0.66309	0.035
41DAP/39DAP	1.01544	1
42DAP/41DAP	0.87369	0.224
43DAP/42DAP	0.89472	0.308
47DAP/43DAP	1.05162	0.934
52DAP/47DAP	1.4621	0.123
57DAP/52DAP	1.07048	0.851
57DAP/7DAP	0.74003	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82334	0.115
17DAP/reference	0.69711	0.011
27DAP/reference	0.77169	0.014
39DAP/reference	0.78735	0.012
41DAP/reference	0.75863	0.013
42DAP/reference	0.78955	0.01
43DAP/reference	0.69499	0.011
47DAP/reference	0.96916	0.671
52DAP/reference	0.73903	0.019
57DAP/reference	0.7464	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47353	0.012
17DAP/reference	0.53102	0.015
27DAP/reference	1.02997	0.619
39DAP/reference	1.37914	0.263
41DAP/reference	1.25848	0.102
42DAP/reference	1.29606	0.016
43DAP/reference	0.80812	0.298
47DAP/reference	0.82566	0.03
52DAP/reference	0.97537	0.576
57DAP/reference	0.49437	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80668	0.043
17DAP/reference	0.76904	0.186
27DAP/reference	0.69576	0.023
39DAP/reference	0.68312	0.014
41DAP/reference	0.83844	0.064
42DAP/reference	1.25113	0.961
43DAP/reference	0.84997	0.197
47DAP/reference	0.96992	0.494
52DAP/reference	0.59364	0.057
57DAP/reference	3.3929	0.075

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25927	0.586
26DAP/20DAP	0.93787	1
34DAP/26DAP	1.13921	1
51DAP/34DAP	1.0069	0.927
52DAP/51DAP	1.30127	0.596
53DAP/52DAP	1.08442	0.738
55DAP/53DAP	1.67925	0.126
57DAP/55DAP	0.93947	0.821
62DAP/57DAP	1.52059	0.515
68DAP/62DAP	5.11198	0.025
68DAP/14DAP	9.6104	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37175	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.72125	0.095
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.37783

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97843	0.944
1-1-2/M82	0.79228
12-2/M82	1.11488
12-4/M82	1.01034	1
1-3/M82	0.68349	0.378
2-1-1/M82	1.13978
2-1/M82	N/A	N/A
2-6/M82	1.02555	1
3-2/M82	N/A	N/A
4-1-1/M82	0.93888	1
4-1/M82	1.30052
4-3-2/M82	N/A	N/A
4-3/M82	0.64103
5-3/M82	0.98728	1
6-2/M82	N/A	N/A
6-3/M82	1.18761
7-1/M82	N/A	N/A
7-2/M82	0.94966	0.881
9-3-2/M82	N/A	N/A

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	0.96359
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.90762	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02205	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.28165
DC3000/delta hrp 24h	0.97187	0.831

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96081	0.724
DC3000 delta B/DC3000 delta AB	0.85795	0.11

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.32483	1
Exp 36h	N/A	N/A
Exp 60h	2.75994	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0363	1
Var 0h	0.9218	0.933
Var 12h I row2-row1	1.20971	0.795
Var 12h NI row2-row1	0.81234	0.36
Var 36h I row2-row1	0.92205	1
Var 36h NI row2-row1	1.05543	1
Var 60h I row2-row1	1.06048	1
Var 60h NI row2-row1	0.98233	1
Time course 0hI-0hNI	1.00937	1
Time course 12hI-12hNI	0.88635	0.089
Time course 36hI-36hNI	0.8461	0.041
Time course 60hI-60hNI	0.23937	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)	1.48206	0.455
transgenic ySAMdc/azygous control (breaker)	0.95301	1
transgenic ySAMdc/azygous control (red)	1.2912	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	4.55645	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03855	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13565	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.36385	0.222