Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.13098	0.24
27DAP/17DAP	1.69082	0.683
39DAP/27DAP	1.56339	0.108
41DAP/39DAP	0.5403	0.041
42DAP/41DAP	0.77653	0.774
43DAP/42DAP	1.03645	1
47DAP/43DAP	0.24265	0.043
52DAP/47DAP	0.95905	0.779
57DAP/52DAP	0.90515	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86024	0.106
17DAP/reference	0.8409	0.12
27DAP/reference	0.94061	0.385
39DAP/reference	0.99331	0.828
41DAP/reference	0.81167	0.026
42DAP/reference	0.86814	0.01
43DAP/reference	1.00451	1
47DAP/reference	0.98421	0.503
52DAP/reference	1.02447	0.668
57DAP/reference	1.14578	0.433

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.56314	0.036
27DAP/17DAP	0.97689	0.887
39DAP/27DAP	1.0379	0.707
41DAP/39DAP	1.30631	1
42DAP/41DAP	0.95153	0.595
43DAP/42DAP	1.61697	0.03
47DAP/43DAP	0.61118	0.02
52DAP/47DAP	1.60814	0.114
57DAP/52DAP	1.40375	0.327
57DAP/7DAP	1.89579	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90206	0.203
17DAP/reference	1.00158	0.693
27DAP/reference	1.1681	0.088
39DAP/reference	1.04842	0.371
41DAP/reference	1.53451	0.126
42DAP/reference	1.15091	0.405
43DAP/reference	1.1324	0.637
47DAP/reference	0.92658	0.168
52DAP/reference	0.96825	0.435
57DAP/reference	1.085	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00551	1
17DAP/reference	0.90367	0.287
27DAP/reference	0.98814	0.619
39DAP/reference	0.91008	0.189
41DAP/reference	1.01176	1
42DAP/reference	0.81306	0.013
43DAP/reference	1.26024	0.356
47DAP/reference	0.85664	0.12
52DAP/reference	1.03962	0.988
57DAP/reference	0.86258	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12262	0.338
17DAP/reference	1.04671	0.572
27DAP/reference	1.05931	0.644
39DAP/reference	1.1012	0.466
41DAP/reference	1.02895	1
42DAP/reference	0.86993	0.22
43DAP/reference	1.16415	0.254
47DAP/reference	0.96637	0.509
52DAP/reference	0.91921	0.455
57DAP/reference	1.02711	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.74816	0.733
26DAP/20DAP	2.15712	0.097
34DAP/26DAP	1.13487	0.819
51DAP/34DAP	1.08763	0.597
52DAP/51DAP	1.21394	0.246
53DAP/52DAP	0.5551	0.071
55DAP/53DAP	0.78153	0.169
57DAP/55DAP	1.35458	0.461
62DAP/57DAP	0.85111	0.28
68DAP/62DAP	1.04218	1
68DAP/14DAP	0.94594	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65593	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55288	0.151
Mature Green Tomato/Ripe Tomato	6.33898	0.015
Immature Eggplant/Mature Eggplant	1.1192	0.278
Ripe Pepper/Ripe Tomato	0.94048	1
Mature Eggplant/Ripe Tomato	1.03311	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04359
1-1-2/M82	1.24602	1
12-2/M82	0.91689
12-4/M82	0.94656	0.358
1-3/M82	0.93587
2-1-1/M82	N/A	N/A
2-1/M82	1.26691
2-6/M82	0.90029	1
3-2/M82	N/A	N/A
4-1-1/M82	1.04449	1
4-1/M82	1.53819
4-3-2/M82	1.60277
4-3/M82	1.0675	1
5-3/M82	1.11661	0.572
6-2/M82	1.03716
6-3/M82	1.04873	1
7-1/M82	N/A	N/A
7-2/M82	1.0979
9-3-2/M82	1.2806	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.98812
IL2-6/WTpooled	1.02611	0.584
IL7-5/WTpooled	0.4509
IL7-3/WTpooled	0.87619	0.294
IL12-4/WTpooled	0.91634	0.71
IL1-4/WTpooled	1.0383	1
WT/WTpooled	0.96208	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	1.05179	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02067	0.921
DC3000/delta hrp 6h	0.80581	0.95
DC3000/delta hrp 12h	0.89572	1
DC3000/delta hrp 24h	1.28675	0.047

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9341	0.92
DC3000 delta B/DC3000 delta AB	1.21695	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95355	1
Exp 36h	1.14319	0.693
Exp 60h	1.09512	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96819	1
Var 0h	1.11633	0.936
Var 12h I row2-row1	0.86478	0.418
Var 12h NI row2-row1	1.02117	1
Var 36h I row2-row1	0.87882	1
Var 36h NI row2-row1	1.26915	1
Var 60h I row2-row1	1.21025	1
Var 60h NI row2-row1	0.93022	0.977
Time course 0hI-0hNI	0.8709	0.076
Time course 12hI-12hNI	1.0104	0.9
Time course 36hI-36hNI	0.84822	0.056
Time course 60hI-60hNI	0.8208	0.047

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)	0.94002	0.3
transgenic ySAMdc/azygous control (breaker)	0.74484	0.137
transgenic ySAMdc/azygous control (red)	0.97187	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11048	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73002	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01373	1
Manapal/WT (break)	0.8956	1
Manapal/WT (red)	0.73989	0.181