Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.3.7.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11528	0.912
27DAP/17DAP	1.57194	0.633
39DAP/27DAP	0.84159	0.482
41DAP/39DAP	1.09311	0.904
42DAP/41DAP	1.29756	0.916
43DAP/42DAP	1.0837	1
47DAP/43DAP	1.10514	0.809
52DAP/47DAP	1.17807	0.913
57DAP/52DAP	0.92655	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.732	0.027
17DAP/reference	0.85256	0.129
27DAP/reference	0.85592	0.106
39DAP/reference	0.88017	0.298
41DAP/reference	0.81957	0.154
42DAP/reference	0.8162	0.019
43DAP/reference	0.90751	0.211
47DAP/reference	0.93177	0.106
52DAP/reference	0.97101	0.489
57DAP/reference	1.02506	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82501	0.454
27DAP/17DAP	0.98411	0.943
39DAP/27DAP	1.12492	0.575
41DAP/39DAP	0.74324	0.547
42DAP/41DAP	0.77848	0.253
43DAP/42DAP	1.20298	N/A
47DAP/43DAP	1.17745	0.848
52DAP/47DAP	0.87799	0.893
57DAP/52DAP	1.4616	0.366
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6275	0.078
17DAP/reference	1.30347	0.269
27DAP/reference	1.42802	0.02
39DAP/reference	0.89205	0.17
41DAP/reference	0.87499	0.146
42DAP/reference	0.80427	0.053
43DAP/reference	0.86888	0.145
47DAP/reference	0.67526	0.035
52DAP/reference	1.09745	0.491
57DAP/reference	0.95304	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95888	0.607
17DAP/reference	0.71267	0.022
27DAP/reference	0.8285	0.134
39DAP/reference	0.83933	0.122
41DAP/reference	0.99445	0.615
42DAP/reference	0.82406	0.169
43DAP/reference	1.10818	1
47DAP/reference	0.68971	0.009
52DAP/reference	1.01013	1
57DAP/reference	0.93444	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09556	0.602
17DAP/reference	1.0959	0.804
27DAP/reference	1.24856	0.081
39DAP/reference	1.16357	0.858
41DAP/reference	1.30413	0.012
42DAP/reference	1.27331	0.175
43DAP/reference	1.17191	0.625
47DAP/reference	0.78429	0.072
52DAP/reference	1.49142	0.158
57DAP/reference	1.02886	0.583

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10037	0.966
26DAP/20DAP	1.01439	1
34DAP/26DAP	1.37126	0.19
51DAP/34DAP	1.18881	N/A
52DAP/51DAP	1.54983	0.089
53DAP/52DAP	2.10969	N/A
55DAP/53DAP	0.83413	0.746
57DAP/55DAP	1.24054	N/A
62DAP/57DAP	1.43053	0.723
68DAP/62DAP	1.33781	N/A
68DAP/14DAP	1.37012	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97158	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	8.86675	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
12-4/M82	0.73669	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	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96243	N/A
IL12-4/WTpooled	0.6227	0.71
IL1-4/WTpooled	1.07344	1
WT/WTpooled	0.78649	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	0.86105	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12734	0.921
DC3000/delta hrp 6h	0.9547	0.95
DC3000/delta hrp 12h	1.25108	1
DC3000/delta hrp 24h	0.83307	0.131

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1228	0.441
DC3000 delta B/DC3000 delta AB	0.98932	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09539	1
Exp 36h	N/A	N/A
Exp 60h	0.78292	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96904	1
Var 0h	0.73443	0.197
Var 12h I row2-row1	0.98324	0.948
Var 12h NI row2-row1	0.93974	0.82
Var 36h I row2-row1	1.13665	0.908
Var 36h NI row2-row1	1.19001	1
Var 60h I row2-row1	0.81996	0.952
Var 60h NI row2-row1	0.94739	1
Time course 0hI-0hNI	0.89095	0.317
Time course 12hI-12hNI	0.93844	0.416
Time course 36hI-36hNI	0.8523	0.114
Time course 60hI-60hNI	0.45242	0.006

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)	29.0056	0.798
transgenic ySAMdc/azygous control (breaker)	1.43284	1
transgenic ySAMdc/azygous control (red)	1.21388	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9314	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40247	0.238

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)	0.90733	0.728