Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11472	0.786
27DAP/17DAP	1.59492	0.646
39DAP/27DAP	0.94049	0.652
41DAP/39DAP	1.11278	0.575
42DAP/41DAP	1.03481	1
43DAP/42DAP	1.01996	0.937
47DAP/43DAP	0.9164	0.699
52DAP/47DAP	1.12809	0.994
57DAP/52DAP	1.07747	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66748	0.025
17DAP/reference	0.91589	0.448
27DAP/reference	1.0383	1
39DAP/reference	0.93423	0.638
41DAP/reference	1.01585	0.963
42DAP/reference	0.74197	0.001
43DAP/reference	0.69165	0.058
47DAP/reference	0.75285	0.027
52DAP/reference	0.9323	0.475
57DAP/reference	2.79714

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44541	0.05
27DAP/17DAP	1.01312	0.919
39DAP/27DAP	1.02345	0.779
41DAP/39DAP	0.83295	0.169
42DAP/41DAP	1.24152	0.539
43DAP/42DAP	0.61462	0.022
47DAP/43DAP	0.88008	0.525
52DAP/47DAP	0.8576	0.572
57DAP/52DAP	1.60341	0.856
57DAP/7DAP	2.72089

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45485	0.057
17DAP/reference	1.09644	1
27DAP/reference	0.95541	0.264
39DAP/reference	0.63203	0.011
41DAP/reference	0.7599	0.064
42DAP/reference	0.64323	0.035
43DAP/reference	1.00402	0.694
47DAP/reference	0.97712	0.671
52DAP/reference	1.07982	0.732
57DAP/reference	0.98247	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76628	0.058
17DAP/reference	0.72083	0.006
27DAP/reference	0.89302	0.366
39DAP/reference	0.9023	0.189
41DAP/reference	0.80825	0.013
42DAP/reference	1.00752	1
43DAP/reference	1.18958	0.89
47DAP/reference	0.88259	0.188
52DAP/reference	0.89509	0.101
57DAP/reference	0.68619	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.78789	0.034
17DAP/reference	1.12009	0.746
27DAP/reference	1.18958	0.072
39DAP/reference	0.93639	0.147
41DAP/reference	0.96973	0.56
42DAP/reference	0.87422	0.108
43DAP/reference	1.10669	0.7
47DAP/reference	0.91198	0.174
52DAP/reference	0.79275	0.123
57DAP/reference	1.42704	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13048	0.966
26DAP/20DAP	1.29277	0.818
34DAP/26DAP	0.95447	0.898
51DAP/34DAP	5.25884	0.026
52DAP/51DAP	1.00925	1
53DAP/52DAP	3.01592	0.024
55DAP/53DAP	1.33156	0.361
57DAP/55DAP	0.61752	0.057
62DAP/57DAP	0.31777	0.002
68DAP/62DAP	1.63183	0.259
68DAP/14DAP	4.96966	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15248	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.27566	0.073
Mature Green Tomato/Ripe Tomato	1.14326	1
Immature Eggplant/Mature Eggplant	0.95506	0.808
Ripe Pepper/Ripe Tomato	12.7502	1
Mature Eggplant/Ripe Tomato	3.82673	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.07467
12-2/M82	N/A	N/A
12-4/M82	0.82704	0.619
1-3/M82	0.90303
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	0.93077	0.752
4-1-1/M82	N/A	N/A
4-1/M82	0.77105
4-3-2/M82	0.91525
4-3/M82	N/A	N/A
5-3/M82	1.72004	0.496
6-2/M82	0.61166	1
6-3/M82	1.44474	0.971
7-1/M82	0.91583
7-2/M82	1.13921	1
9-3-2/M82	0.7821	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.44764	0.277
IL2-6/WTpooled	1.19727	0.531
IL7-5/WTpooled	1.50835	0.792
IL7-3/WTpooled	1.69482	1
IL12-4/WTpooled	0.89983	1
IL1-4/WTpooled	1.19507	1
WT/WTpooled	0.92326	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	0.89626

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11228	0.921
DC3000/delta hrp 6h	1.03468	1
DC3000/delta hrp 12h	1.09045	1
DC3000/delta hrp 24h	0.82397	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54691
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11854	1
Exp 36h	0.95611	0.82
Exp 60h	1.07422	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96815	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.90192	0.344
Var 12h NI row2-row1	1.09725	0.649
Var 36h I row2-row1	1.24557	0.41
Var 36h NI row2-row1	1.00162	0.852
Var 60h I row2-row1	0.6612	0.293
Var 60h NI row2-row1	0.93809	1
Time course 0hI-0hNI	0.97189	0.829
Time course 12hI-12hNI	1.01382	1
Time course 36hI-36hNI	1.15934	0.28
Time course 60hI-60hNI	2.07046	0.008

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)	1.00492	1
transgenic ySAMdc/azygous control (breaker)	0.86092	0.15
transgenic ySAMdc/azygous control (red)	0.9687	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13785	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14727	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85345	0.172
Manapal/WT (break)	0.80558	1
Manapal/WT (red)	0.87856	0.424