Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32215	0.755
27DAP/17DAP	0.93371	0.877
39DAP/27DAP	2.50572	0.04
41DAP/39DAP	0.79457	0.24
42DAP/41DAP	0.71131	0.774
43DAP/42DAP	1.14331	1
47DAP/43DAP	0.5794	0.064
52DAP/47DAP	2.7491	0.136
57DAP/52DAP	1.13355	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00745	0.526
17DAP/reference	0.84046	0.208
27DAP/reference	0.95199	0.552
39DAP/reference	1.0123	0.611
41DAP/reference	0.56592	0.021
42DAP/reference	1.879	0.001
43DAP/reference	1.44972	0.02
47DAP/reference	1.10355	0.254
52DAP/reference	1.02057	0.598
57DAP/reference	1.24043	0.079

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63829	0.096
27DAP/17DAP	0.98301	0.854
39DAP/27DAP	1.38476	0.373
41DAP/39DAP	0.7094	0.158
42DAP/41DAP	1.53969	0.027
43DAP/42DAP	1.30828	0.038
47DAP/43DAP	1.02881	0.857
52DAP/47DAP	0.5062	0.045
57DAP/52DAP	1.14856	0.368
57DAP/7DAP	1.23535	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81077	0.024
17DAP/reference	1.1853	0.009
27DAP/reference	1.88915	0.006
39DAP/reference	1.10371	0.175
41DAP/reference	1.56867	0.019
42DAP/reference	2.58708	0.007
43DAP/reference	3.73209	0.006
47DAP/reference	3.06294	0.014
52DAP/reference	2.27184	0.007
57DAP/reference	0.94932	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95602	0.607
17DAP/reference	0.85237	0.176
27DAP/reference	1.51056	0.067
39DAP/reference	1.22722	0.207
41DAP/reference	1.20057	0.027
42DAP/reference	1.40854	0.009
43DAP/reference	0.597	0.018
47DAP/reference	0.82743	0.033
52DAP/reference	0.46228	0.003
57DAP/reference	0.39618	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36535	0.052
17DAP/reference	0.7726	0.144
27DAP/reference	1.29674	0.034
39DAP/reference	2.3421	0.01
41DAP/reference	1.49035	0.008
42DAP/reference	2.99096	0.006
43DAP/reference	3.34005	0.007
47DAP/reference	0.83692	0.207
52DAP/reference	1.81744	0.031
57DAP/reference	1.67402	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97832	1
26DAP/20DAP	1.17392	0.735
34DAP/26DAP	0.9351	0.861
51DAP/34DAP	1.96478	0.031
52DAP/51DAP	0.65245	0.151
53DAP/52DAP	2.5712	0.023
55DAP/53DAP	0.56998	0.016
57DAP/55DAP	0.90605	0.688
62DAP/57DAP	0.67662	0.01
68DAP/62DAP	2.11821	0.036
68DAP/14DAP	1.94833	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.26417	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79571	0.251
Mature Green Tomato/Ripe Tomato	0.70174	0.042
Immature Eggplant/Mature Eggplant	1.13087	0.074
Ripe Pepper/Ripe Tomato	0.55221	0.293
Mature Eggplant/Ripe Tomato	0.48347	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.27653	0.877
1-1-2/M82	1.04863	1
12-2/M82	0.99106	1
12-4/M82	1.2555	1
1-3/M82	3.13246	0.26
2-1-1/M82	0.93665	0.92
2-1/M82	0.74658	0.322
2-6/M82	1.14215	0.329
3-2/M82	0.9972	1
4-1-1/M82	1.07516
4-1/M82	1.73794	1
4-3-2/M82	1.89351	0.262
4-3/M82	1.01599	1
5-3/M82	1.21655	1
6-2/M82	1.64765	0.253
6-3/M82	0.97246	1
7-1/M82	0.96865	1
7-2/M82	1.74935	0.385
9-3-2/M82	2.86004	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77812	0.321
IL2-6/WTpooled	1.0607	0.584
IL7-5/WTpooled	0.83832	1
IL7-3/WTpooled	1.15219	1
IL12-4/WTpooled	1.11713	0.531
IL1-4/WTpooled	1.03185	1
WT/WTpooled	1.04505	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	0.9818	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85533	0.541
DC3000/delta hrp 6h	1.08257
DC3000/delta hrp 12h	1.12931	1
DC3000/delta hrp 24h	0.90782	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.38198	0.023
DC3000 delta B/DC3000 delta AB	0.35997	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09821	1
Exp 36h	1.04617	1
Exp 60h	1.06152	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98253	1
Var 0h	0.4554	0.291
Var 12h I row2-row1	0.67537	0.338
Var 12h NI row2-row1	0.90304	0.494
Var 36h I row2-row1	0.80772	0.438
Var 36h NI row2-row1	1.19637	1
Var 60h I row2-row1	1.19644	0.543
Var 60h NI row2-row1	1.03635	1
Time course 0hI-0hNI	0.94692	0.687
Time course 12hI-12hNI	1.05434	0.682
Time course 36hI-36hNI	0.80258	0.023
Time course 60hI-60hNI	0.15968	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)	1.09256	0.699
transgenic ySAMdc/azygous control (breaker)	0.99478	1
transgenic ySAMdc/azygous control (red)	0.89883	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.66805	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01416	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11516	0.307
Manapal/WT (break)	1.062	0.14
Manapal/WT (red)	1.02689	1