Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83514	0.395
27DAP/17DAP	1.05681	0.922
39DAP/27DAP	0.8384	0.529
41DAP/39DAP	1.29837	0.676
42DAP/41DAP	1.15338	0.899
43DAP/42DAP	1.2867	0.595
47DAP/43DAP	0.87199	0.591
52DAP/47DAP	1.24424	0.556
57DAP/52DAP	1.05789	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84908	0.128
17DAP/reference	0.74404	0.091
27DAP/reference	0.76939	0.011
39DAP/reference	0.87869	0.487
41DAP/reference	1.08933	0.714
42DAP/reference	0.86109	0.196
43DAP/reference	0.80743
47DAP/reference	0.92532	0.191
52DAP/reference	0.92004	0.319
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91878	0.526
27DAP/17DAP	1.02535	1
39DAP/27DAP	1.06878	0.77
41DAP/39DAP	0.91018	0.645
42DAP/41DAP	1.10162	0.74
43DAP/42DAP	1.2704	0.162
47DAP/43DAP	1.07706	0.901
52DAP/47DAP	0.83605	0.645
57DAP/52DAP	0.97681	0.793
57DAP/7DAP	0.77843	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95707	0.361
17DAP/reference	1.03279	0.574
27DAP/reference	1.09674	0.197
39DAP/reference	1.10945	0.133
41DAP/reference	1.02557	1
42DAP/reference	0.90548	0.222
43DAP/reference	1.01395	1
47DAP/reference	0.98528	0.671
52DAP/reference	0.94122	0.213
57DAP/reference	0.90152	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36935	0.113
17DAP/reference	1.37067	0.066
27DAP/reference	1.09922	0.412
39DAP/reference	0.98144	0.526
41DAP/reference	0.95277	0.262
42DAP/reference	1.23112	0.254
43DAP/reference	1.18909	0.072
47DAP/reference	0.95781	0.423
52DAP/reference	0.89117
57DAP/reference	1.00684	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03658	0.616
17DAP/reference	1.06342	0.563
27DAP/reference	1.3108	0.035
39DAP/reference	1.03359	0.528
41DAP/reference	1.14385	0.04
42DAP/reference	1.08835	0.47
43DAP/reference	1.11932	0.32
47DAP/reference	0.85538	0.06
52DAP/reference	0.95317	0.573
57DAP/reference	0.93069	0.161

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86366	0.733
26DAP/20DAP	0.98139	1
34DAP/26DAP	0.95773	0.944
51DAP/34DAP	0.93154	0.722
52DAP/51DAP	1.17632	0.836
53DAP/52DAP	1.06857	1
55DAP/53DAP	1.27796	0.087
57DAP/55DAP	1.02609	0.921
62DAP/57DAP	0.99723	1
68DAP/62DAP	1.57956	0.616
68DAP/14DAP	2.15226	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.42313	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.43934
Mature Green Tomato/Ripe Tomato	0.82081
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	6.49967
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07758	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
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	0.83542
3-2/M82	1.10037
4-1-1/M82	N/A	N/A
4-1/M82	1.60195
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96748	1
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	0.94556	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.9974
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.98457
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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0668	0.875
DC3000/delta hrp 6h	1.90686	0.978
DC3000/delta hrp 12h	1.12727	1
DC3000/delta hrp 24h	1.02118	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.4123
DC3000 delta B/DC3000 delta AB	0.96588

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.4647	1
Exp 36h	0.25438	1
Exp 60h	1.29955	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99726	1
Var 0h	1.08117	0.594
Var 12h I row2-row1	1.06119	0.613
Var 12h NI row2-row1	0.8234
Var 36h I row2-row1	1.04058
Var 36h NI row2-row1	0.82375	0.478
Var 60h I row2-row1	0.97781	0.952
Var 60h NI row2-row1	0.65961	1
Time course 0hI-0hNI	0.93762	0.618
Time course 12hI-12hNI	1.0912	0.82
Time course 36hI-36hNI	1.10535	0.248
Time course 60hI-60hNI	3.52083	0.029

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)	1.14605	0.347
transgenic ySAMdc/azygous control (breaker)	1.17649	1
transgenic ySAMdc/azygous control (red)	1.11233	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9776	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8368	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18268	0.307
Manapal/WT (break)	1.10649	1
Manapal/WT (red)	0.89169	0.36