Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.41677	0.014
27DAP/17DAP	0.54763	0.04
39DAP/27DAP	0.76671	0.512
41DAP/39DAP	0.77411	0.285
42DAP/41DAP	1.01296	1
43DAP/42DAP	0.98523	0.931
47DAP/43DAP	1.06721	0.943
52DAP/47DAP	0.97452	0.832
57DAP/52DAP	1.04833	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4445	0.015
17DAP/reference	1.2858	0.016
27DAP/reference	1.77978	0.015
39DAP/reference	0.9077	0.124
41DAP/reference	0.80222	0.039
42DAP/reference	0.93167	0.103
43DAP/reference	0.78754	0.015
47DAP/reference	0.90462	0.071
52DAP/reference	0.85089	0.139
57DAP/reference	1.02442	0.621

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.38157	0.02
27DAP/17DAP	1.74235	0.027
39DAP/27DAP	0.61132	0.029
41DAP/39DAP	0.48513	0.019
42DAP/41DAP	1.14828	0.836
43DAP/42DAP	1.02058	0.788
47DAP/43DAP	0.95676	0.855
52DAP/47DAP	1.01069	0.973
57DAP/52DAP	1.00474	0.929
57DAP/7DAP	0.60498	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.63248	0.037
17DAP/reference	1.19468	0.162
27DAP/reference	0.91935	0.248
39DAP/reference	0.87418	0.198
41DAP/reference	0.98738	0.565
42DAP/reference	1.15774	0.308
43DAP/reference	0.75242	0.056
47DAP/reference	0.74693	0.036
52DAP/reference	0.77261	0.106
57DAP/reference	0.78056	0.048

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08583	0.67
17DAP/reference	1.26241	0.028
27DAP/reference	0.97809	0.537
39DAP/reference	0.69648	0.008
41DAP/reference	0.89147	0.049
42DAP/reference	0.96278	0.261
43DAP/reference	0.74155	0.021
47DAP/reference	0.7394	0.015
52DAP/reference	0.84988	0.016
57DAP/reference	0.6983	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.39597	0.015
17DAP/reference	1.5385	0.091
27DAP/reference	1.59115	0.025
39DAP/reference	0.94541	0.393
41DAP/reference	0.98476	0.682
42DAP/reference	1.0088	1
43DAP/reference	0.84368	0.027
47DAP/reference	0.69715	0.004
52DAP/reference	0.7048	0.055
57DAP/reference	0.92896	0.154

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12849	0.966
26DAP/20DAP	1.4677	0.166
34DAP/26DAP	0.87156	0.412
51DAP/34DAP	1.1405	0.637
52DAP/51DAP	0.93121	1
53DAP/52DAP	0.82814	0.329
55DAP/53DAP	0.83891	0.313
57DAP/55DAP	1.0175	0.911
62DAP/57DAP	1.03647	1
68DAP/62DAP	1.2581	0.188
68DAP/14DAP	1.22848	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.22807	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0608	0.666
Mature Green Tomato/Ripe Tomato	7.85711	0.015
Immature Eggplant/Mature Eggplant	0.42618	0.062
Ripe Pepper/Ripe Tomato	33.5054	0.258
Mature Eggplant/Ripe Tomato	22	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06629	1
1-1-2/M82	0.99855
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	0.62829
2-1-1/M82	N/A	N/A
2-1/M82	1.11285
2-6/M82	1.08608	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.73767
4-1/M82	2.01787
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.92966	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96852
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	1.04077	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78316	0.418
IL12-4/WTpooled	0.83283	0.71
IL1-4/WTpooled	0.94221
WT/WTpooled	1.00634	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	0.84588	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02702	0.914
DC3000/delta hrp 6h	1.13373	1
DC3000/delta hrp 12h	1.20161	1
DC3000/delta hrp 24h	0.60368	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44575	0.023
DC3000 delta B/DC3000 delta AB	0.51752	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.019	1
Exp 36h	0.76777	0.539
Exp 60h	0.60318	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97885	1
Var 0h	0.74591	1
Var 12h I row2-row1	0.92891	0.565
Var 12h NI row2-row1	0.99503	1
Var 36h I row2-row1	1.03686	1
Var 36h NI row2-row1	1.2048	1
Var 60h I row2-row1	0.90367	0.832
Var 60h NI row2-row1	1.11349	0.904
Time course 0hI-0hNI	0.99178	1
Time course 12hI-12hNI	0.90762	0.357
Time course 36hI-36hNI	0.72752	0.023
Time course 60hI-60hNI	0.1427	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)	0.84354	0.428
transgenic ySAMdc/azygous control (breaker)	1.55926	0.172
transgenic ySAMdc/azygous control (red)	1.03271	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.78573	0.09

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.6137	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.42565	0.14
Manapal/WT (break)	1.13013	1
Manapal/WT (red)	1.60634	0.137