Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.1.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02187	0.977
27DAP/17DAP	1.20226	0.815
39DAP/27DAP	0.98411	0.733
41DAP/39DAP	0.96406	0.781
42DAP/41DAP	0.97747	1
43DAP/42DAP	0.83561	0.7
47DAP/43DAP	0.80146	0.407
52DAP/47DAP	1.14103	0.867
57DAP/52DAP	1.45425	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94528	0.293
17DAP/reference	0.81559	0.016
27DAP/reference	1.01463	0.966
39DAP/reference	0.86748	0.07
41DAP/reference	0.78626	0.039
42DAP/reference	1.07397	0.544
43DAP/reference	0.94973	0.302
47DAP/reference	1.18085	0.039
52DAP/reference	1.24892	0.035
57DAP/reference	1.17753	0.166

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12518	0.464
27DAP/17DAP	1.1559	0.423
39DAP/27DAP	0.87307	0.243
41DAP/39DAP	1.09949	0.294
42DAP/41DAP	0.92134	0.407
43DAP/42DAP	1.01705	1
47DAP/43DAP	0.98242	0.919
52DAP/47DAP	1.05564	0.785
57DAP/52DAP	0.96038	0.709
57DAP/7DAP	1.1523	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62017	0.066
17DAP/reference	0.50099	0.011
27DAP/reference	0.8578	0.058
39DAP/reference	0.46916	0.013
41DAP/reference	0.43998	0.02
42DAP/reference	0.42921	0.01
43DAP/reference	0.47802	0.012
47DAP/reference	0.83153	0.293
52DAP/reference	0.42712	0.011
57DAP/reference	0.6061	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93963	0.457
17DAP/reference	1.01687	0.898
27DAP/reference	1.25373	0.093
39DAP/reference	1.30262	0.068
41DAP/reference	1.44428	0.011
42DAP/reference	1.31871	0.014
43DAP/reference	0.94638	0.45
47DAP/reference	0.9981	0.73
52DAP/reference	1.24804	0.036
57DAP/reference	1.00521	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7237	0.074
17DAP/reference	0.90422	0.417
27DAP/reference	0.8345	0.126
39DAP/reference	0.80998	0.069
41DAP/reference	0.79471	0.02
42DAP/reference	0.86463	0.287
43DAP/reference	0.8769	0.281
47DAP/reference	1.21482	0.093
52DAP/reference	0.9059	0.464
57DAP/reference	1.57193	0.077

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87879	0.997
26DAP/20DAP	0.97448	1
34DAP/26DAP	0.83835	0.472
51DAP/34DAP	1.1432	0.496
52DAP/51DAP	0.98935	1
53DAP/52DAP	1.29601	0.204
55DAP/53DAP	0.9716	0.796
57DAP/55DAP	1.19588	0.694
62DAP/57DAP	1.17324
68DAP/62DAP	1.14262	0.858
68DAP/14DAP	1.4122	0.094

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68666	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8871	0.39
Mature Green Tomato/Ripe Tomato	1.51888	0.523
Immature Eggplant/Mature Eggplant	1.1414	0.066
Ripe Pepper/Ripe Tomato	0.96006	1
Mature Eggplant/Ripe Tomato	0.95863	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00365	1
1-1-2/M82	0.96139
12-2/M82	1.0387	1
12-4/M82	1.02341	1
1-3/M82	1.08367	1
2-1-1/M82	1.12004	0.689
2-1/M82	1.35765	1
2-6/M82	1.03325	0.505
3-2/M82	1.03542
4-1-1/M82	0.97799	1
4-1/M82	1.12338
4-3-2/M82	0.76386
4-3/M82	0.8737	1
5-3/M82	1.0272	1
6-2/M82	0.86746
6-3/M82	0.95671	1
7-1/M82	1.06776	1
7-2/M82	1.0047	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93777	1
IL2-6/WTpooled	0.90698	1
IL7-5/WTpooled	0.75771	1
IL7-3/WTpooled	2.19718	1
IL12-4/WTpooled	1.04075	0.839
IL1-4/WTpooled	0.96708	0.699
WT/WTpooled	1.10503	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	1.02716	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03283	0.921
DC3000/delta hrp 6h	0.9843	0.95
DC3000/delta hrp 12h	1.00074	1
DC3000/delta hrp 24h	0.97148	0.808

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.90153

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16115	1
Exp 36h	0.90098	0.589
Exp 60h	1.03103	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9626	1
Var 0h	1.29378	0.594
Var 12h I row2-row1	0.80602	0.705
Var 12h NI row2-row1	0.90537	0.488
Var 36h I row2-row1	0.67793	0.805
Var 36h NI row2-row1	1.35771	0.482
Var 60h I row2-row1	1.01467	1
Var 60h NI row2-row1	1.10251	1
Time course 0hI-0hNI	0.88277	0.188
Time course 12hI-12hNI	1.00203	1
Time course 36hI-36hNI	0.86991	0.045
Time course 60hI-60hNI	0.33516	0.006

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)	1.07393	0.541
transgenic ySAMdc/azygous control (breaker)	0.59806	0.142
transgenic ySAMdc/azygous control (red)	1.08866	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94608	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.47413	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.037	0.083
Manapal/WT (break)	1.47525	0.14
Manapal/WT (red)	1.60181	1