Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87842	0.405
27DAP/17DAP	1.16094	0.833
39DAP/27DAP	1.14115	0.74
41DAP/39DAP	1.10882	0.516
42DAP/41DAP	1.08562	0.929
43DAP/42DAP	1.05111	1
47DAP/43DAP	1.25597	0.542
52DAP/47DAP	0.87645	0.682
57DAP/52DAP	1.15873	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	N/A	N/A
27DAP/reference	1.48505
39DAP/reference	N/A	N/A
41DAP/reference	N/A	N/A
42DAP/reference	1.16609	0.125
43DAP/reference	0.85715
47DAP/reference	1.15856	1
52DAP/reference	1.19049
57DAP/reference	0.52118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95557	0.484
27DAP/17DAP	1.02897	0.9
39DAP/27DAP	1.02214	0.659
41DAP/39DAP	1.04528	0.565
42DAP/41DAP	1.01395	1
43DAP/42DAP	0.98417	0.774
47DAP/43DAP	1.0036	0.973
52DAP/47DAP	1.00269	1
57DAP/52DAP	1.07499	0.504
57DAP/7DAP	0.99357	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90922	0.224
17DAP/reference	1.16862	0.328
27DAP/reference	1.48293	0.02
39DAP/reference	1.78338	0.016
41DAP/reference	1.87668	0.016
42DAP/reference	1.64006	0.686
43DAP/reference	1.44155	0.011
47DAP/reference	1.12825	0.279
52DAP/reference	1.40823	0.01
57DAP/reference	1.45869	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20206	0.249
17DAP/reference	1.41571	0.03
27DAP/reference	1.18165	0.163
39DAP/reference	1.35882	0.018
41DAP/reference	1.31637	0.037
42DAP/reference	1.19177	0.023
43DAP/reference	1.07807	0.728
47DAP/reference	1.35631	0.008
52DAP/reference	1.3221	0.006
57DAP/reference	1.43264	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54992	0.034
17DAP/reference	1.09383	0.833
27DAP/reference	1.3531	0.054
39DAP/reference	1.31348	0.009
41DAP/reference	1.36249	0.034
42DAP/reference	1.49713	0.014
43DAP/reference	1.46877	0.062
47DAP/reference	1.30634	0.179
52DAP/reference	1.74848	0.087
57DAP/reference	1.13843	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.76694	0.981
26DAP/20DAP	0.95027	0.512
34DAP/26DAP	0.99705	1
51DAP/34DAP	1.02319	0.84
52DAP/51DAP	1.0102	0.925
53DAP/52DAP	0.99956	1
55DAP/53DAP	0.99127	0.876
57DAP/55DAP	1.08234	0.898
62DAP/57DAP	1.09539	0.868
68DAP/62DAP	0.58404	0.05
68DAP/14DAP	0.8732	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94986	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.16911
Mature Green Tomato/Ripe Tomato	0.58815	0.04
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.23636
Mature Eggplant/Ripe Tomato	1.14891	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85274
1-1-2/M82	1.07332	1
12-2/M82	0.77972	0.678
12-4/M82	0.6923	0.274
1-3/M82	N/A	N/A
2-1-1/M82	1.1055	1
2-1/M82	0.86785	0.74
2-6/M82	0.88002	0.421
3-2/M82	0.93895
4-1-1/M82	N/A	N/A
4-1/M82	1.13151
4-3-2/M82	N/A	N/A
4-3/M82	1.26209	1
5-3/M82	1.27936	0.467
6-2/M82	N/A	N/A
6-3/M82	1.02319	1
7-1/M82	0.85087
7-2/M82	1.16764	0.385
9-3-2/M82	1.33834

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.25797	0.277
IL2-6/WTpooled	0.82542	1
IL7-5/WTpooled	1.04553	1
IL7-3/WTpooled	2.71879	1
IL12-4/WTpooled	1.38179	0.595
IL1-4/WTpooled	2.20739	1
WT/WTpooled	0.92451	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	0.97446	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05039	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.2093	1
DC3000/delta hrp 24h	1.04421	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99841	1
DC3000 delta B/DC3000 delta AB	0.95612	0.483

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01061	1
Var 0h	0.9107	1
Var 12h I row2-row1	0.96634	0.565
Var 12h NI row2-row1	0.90931	0.488
Var 36h I row2-row1	1.01447	1
Var 36h NI row2-row1	1.00472	1
Var 60h I row2-row1	1.13896	1
Var 60h NI row2-row1	0.92871	0.866
Time course 0hI-0hNI	1.0003	1
Time course 12hI-12hNI	0.96984	0.556
Time course 36hI-36hNI	0.99153	0.654
Time course 60hI-60hNI	0.60551	0.011

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.98389	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85426	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29851	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.57019	0.222