Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00883	0.847
27DAP/17DAP	1.15324	0.873
39DAP/27DAP	0.61967	0.216
41DAP/39DAP	1.33047	0.934
42DAP/41DAP	0.8159	1
43DAP/42DAP	1.14107	0.991
47DAP/43DAP	0.99643	0.746
52DAP/47DAP	1.00286	0.806
57DAP/52DAP	1.02498	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98837	0.661
17DAP/reference	1.03477	0.294
27DAP/reference	1.03631	0.548
39DAP/reference	0.93094	0.068
41DAP/reference	0.95905	0.542
42DAP/reference	0.86955	0.003
43DAP/reference	0.91359	0.093
47DAP/reference	0.90159	0.055
52DAP/reference	0.83822	0.033
57DAP/reference	0.89663	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00933	1
27DAP/17DAP	0.99962	0.969
39DAP/27DAP	0.9958	1
41DAP/39DAP	1.37097	0.531
42DAP/41DAP	0.76478	0.025
43DAP/42DAP	0.74821	0.025
47DAP/43DAP	0.91771	0.588
52DAP/47DAP	1.13118	0.549
57DAP/52DAP	1.47289	0.05
57DAP/7DAP	1.01839	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94215	0.27
17DAP/reference	1.198	0.028
27DAP/reference	0.90802	0.117
39DAP/reference	1.00889	1
41DAP/reference	1.01988	1
42DAP/reference	1.19955	0.174
43DAP/reference	1.07627	0.483
47DAP/reference	0.96811	0.671
52DAP/reference	0.97316	0.477
57DAP/reference	0.89568	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02445	0.979
17DAP/reference	0.93794	0.337
27DAP/reference	0.88488	0.155
39DAP/reference	0.78819	0.02
41DAP/reference	0.86699	0.112
42DAP/reference	0.86151	0.046
43DAP/reference	0.94042	0.394
47DAP/reference	0.89918	0.149
52DAP/reference	0.93874	0.171
57DAP/reference	0.99731	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03467	1
17DAP/reference	0.93382	0.528
27DAP/reference	0.82638	0.319
39DAP/reference	0.69747	0.037
41DAP/reference	0.85459	0.064
42DAP/reference	0.99631	1
43DAP/reference	0.7196	0.031
47DAP/reference	0.91595	0.093
52DAP/reference	0.89954	0.368
57DAP/reference	0.83199	0.054

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15683	0.878
26DAP/20DAP	1.16249	0.855
34DAP/26DAP	1.30264	0.304
51DAP/34DAP	0.78235	0.167
52DAP/51DAP	1.48898	0.055
53DAP/52DAP	1.04623	0.961
55DAP/53DAP	1.13075	0.703
57DAP/55DAP	0.82936	0.327
62DAP/57DAP	1.3033	0.303
68DAP/62DAP	0.94105	0.747
68DAP/14DAP	1.0377	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54753	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82047
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	4.23404
Ripe Pepper/Ripe Tomato	0.44753	0.224
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.8618
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	N/A	N/A
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	1.04531
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83537	0.321
IL2-6/WTpooled	1.1293	0.427
IL7-5/WTpooled	0.9155	1
IL7-3/WTpooled	0.85221	0.418
IL12-4/WTpooled	1.28068	0.516
IL1-4/WTpooled	0.79594	0.562
WT/WTpooled	1.3323	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	0.63889

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02548	0.921
DC3000/delta hrp 6h	1.16387	0.95
DC3000/delta hrp 12h	0.99702	1
DC3000/delta hrp 24h	1.06286	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78167
DC3000 delta B/DC3000 delta AB	0.87428	0.393

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.73988	1
Exp 36h	0.936	0.82
Exp 60h	0.94408	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02515	1
Var 0h	1.12083	0.782
Var 12h I row2-row1	0.93123	0.856
Var 12h NI row2-row1	0.90609	0.394
Var 36h I row2-row1	1.02052	1
Var 36h NI row2-row1	0.99334	0.852
Var 60h I row2-row1	1.00748	1
Var 60h NI row2-row1	0.70484	0.904
Time course 0hI-0hNI	0.90264	0.381
Time course 12hI-12hNI	0.92726	0.497
Time course 36hI-36hNI	0.98349	0.665
Time course 60hI-60hNI	0.70839	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)	0.99345	0.862
transgenic ySAMdc/azygous control (breaker)	1.04147	1
transgenic ySAMdc/azygous control (red)	0.99156	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03099	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29706	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8458	1
Manapal/WT (break)	0.93783	1
Manapal/WT (red)	1.41817	0.222