Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32536	0.414
27DAP/17DAP	1.7921	0.588
39DAP/27DAP	1.06961	0.919
41DAP/39DAP	1.18888	0.758
42DAP/41DAP	1.19895	0.722
43DAP/42DAP	1.26991	0.724
47DAP/43DAP	1.83012	0.52
52DAP/47DAP	1.38385	0.588
57DAP/52DAP	1.04952	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84705	0.103
17DAP/reference	1.16174	0.306
27DAP/reference	0.87214	0.369
39DAP/reference	0.81674	0.026
41DAP/reference	0.95144	0.667
42DAP/reference	0.92976	0.016
43DAP/reference	1.01721
47DAP/reference	0.93838	0.392
52DAP/reference	0.97491	0.504
57DAP/reference	0.36071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00316	0.847
27DAP/17DAP	1.32881	0.089
39DAP/27DAP	0.94818	0.622
41DAP/39DAP	1.04655	0.817
42DAP/41DAP	0.95858	0.674
43DAP/42DAP	0.94108	0.466
47DAP/43DAP	1.018	0.99
52DAP/47DAP	1.03535	0.868
57DAP/52DAP	1.07665	0.674
57DAP/7DAP	1.36898	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59383	0.033
17DAP/reference	2.14888	0.006
27DAP/reference	1.77878	0.007
39DAP/reference	2.35738	0.005
41DAP/reference	2.17375	0.011
42DAP/reference	2.24367	0.008
43DAP/reference	2.02275	0.007
47DAP/reference	1.3165	0.127
52DAP/reference	1.799	0.019
57DAP/reference	1.84745	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92934	0.277
17DAP/reference	0.89706	0.106
27DAP/reference	0.92227	0.115
39DAP/reference	1.00851	1
41DAP/reference	1.03922	0.629
42DAP/reference	0.93971	0.089
43DAP/reference	0.74142	0.022
47DAP/reference	0.93937	0.012
52DAP/reference	1.00467	1
57DAP/reference	0.94844	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54856	0.031
17DAP/reference	1.3923	0.283
27DAP/reference	1.7156	0.034
39DAP/reference	1.52443	0.041
41DAP/reference	1.97938	0.011
42DAP/reference	1.88891	0.037
43DAP/reference	1.47185	0.096
47DAP/reference	0.95588	0.409
52DAP/reference	1.76066	0.088
57DAP/reference	1.32923	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0302	0.966
26DAP/20DAP	1.27636	0.487
34DAP/26DAP	0.76426	0.472
51DAP/34DAP	1.39762	0.377
52DAP/51DAP	0.94093	1
53DAP/52DAP	0.98927	0.938
55DAP/53DAP	1.13431	0.622
57DAP/55DAP	1.04079	0.875
62DAP/57DAP	0.78912	0.681
68DAP/62DAP	0.902	0.7
68DAP/14DAP	1.03981	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.5761	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18502	0.417
Mature Green Tomato/Ripe Tomato	1.1687	0.478
Immature Eggplant/Mature Eggplant	1.17352	0.181
Ripe Pepper/Ripe Tomato	0.82104	1
Mature Eggplant/Ripe Tomato	0.79128	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9533	0.961
1-1-2/M82	0.85529
12-2/M82	N/A	N/A
12-4/M82	0.89957
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	1.28763
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.06281	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	1.11618
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	N/A	N/A
IL7-5/WTpooled	0.30772
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.01187	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98544	1
DC3000/delta hrp 6h	0.95921	0.95
DC3000/delta hrp 12h	0.95657	1
DC3000/delta hrp 24h	1.00569	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87875	0.273
DC3000 delta B/DC3000 delta AB	1.57258	0.368

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94028	0.328
Exp 36h	0.79571	0.504
Exp 60h	0.80662	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.97396	1
Var 12h I row2-row1	1.16215	0.473
Var 12h NI row2-row1	1.04259	1
Var 36h I row2-row1	0.74678	0.34
Var 36h NI row2-row1	1.18742	1
Var 60h I row2-row1	0.85772	0.374
Var 60h NI row2-row1	0.96858	1
Time course 0hI-0hNI	0.92462	0.745
Time course 12hI-12hNI	1.01204	0.876
Time course 36hI-36hNI	1.38921	0.007
Time course 60hI-60hNI	1.42432	0.012

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)	0.86367	0.315
transgenic ySAMdc/azygous control (breaker)	0.82398	0.15
transgenic ySAMdc/azygous control (red)	0.99423	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00234	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2714	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81822	0.172
Manapal/WT (break)	0.85765	0.333
Manapal/WT (red)	1.15927	0.413