Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97033	0.77
27DAP/17DAP	0.68813	0.18
39DAP/27DAP	0.77704	0.364
41DAP/39DAP	1.20093	0.753
42DAP/41DAP	1.17805	0.599
43DAP/42DAP	2.11312	0.028
47DAP/43DAP	1.45848	0.216
52DAP/47DAP	0.69641	0.325
57DAP/52DAP	1.00292	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03292	0.994
17DAP/reference	1.11062	0.306
27DAP/reference	1.1344	0.205
39DAP/reference	0.97712	0.72
41DAP/reference	1.1026	0.338
42DAP/reference	0.92764	0.072
43DAP/reference	1.02425	0.928
47DAP/reference	1.00716	1
52DAP/reference	0.96152	0.405
57DAP/reference	0.92348	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.41563	0.049
27DAP/17DAP	0.86673	0.259
39DAP/27DAP	0.83189	0.239
41DAP/39DAP	0.7981	0.147
42DAP/41DAP	1.05996	0.976
43DAP/42DAP	1.13599	0.351
47DAP/43DAP	1.01641	0.969
52DAP/47DAP	1.12359	0.603
57DAP/52DAP	1.18254	0.483
57DAP/7DAP	1.10086	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04773	0.776
17DAP/reference	0.86393	0.064
27DAP/reference	0.87737	0.071
39DAP/reference	1.09279	0.186
41DAP/reference	0.8541	0.023
42DAP/reference	0.80025	0.07
43DAP/reference	0.8726	0.175
47DAP/reference	0.89693	0.293
52DAP/reference	0.9118	0.126
57DAP/reference	0.88049	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15334	0.443
17DAP/reference	1.0594	0.708
27DAP/reference	0.84255	0.044
39DAP/reference	0.93211	0.33
41DAP/reference	1.19094	0.781
42DAP/reference	0.971	0.433
43DAP/reference	0.90041	0.212
47DAP/reference	1.05145	0.282
52DAP/reference	0.89781	0.156
57DAP/reference	0.98447	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30106	0.027
17DAP/reference	0.909	0.234
27DAP/reference	0.95345	0.397
39DAP/reference	0.88296	0.063
41DAP/reference	1.09529	0.486
42DAP/reference	0.90018	0.287
43DAP/reference	1.00966	1
47DAP/reference	0.8851	0.125
52DAP/reference	1.03609	0.904
57DAP/reference	1.2012	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92823	1
26DAP/20DAP	0.98083	1
34DAP/26DAP	0.88377	0.462
51DAP/34DAP	1.88487	0.041
52DAP/51DAP	0.88868	1
53DAP/52DAP	1.63317	0.117
55DAP/53DAP	1.04717	0.722
57DAP/55DAP	1.17927	0.584
62DAP/57DAP	0.52026	0.002
68DAP/62DAP	0.85495	0.668
68DAP/14DAP	0.77657	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62268	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.41181	0.078
Mature Green Tomato/Ripe Tomato	0.63117	0.256
Immature Eggplant/Mature Eggplant	0.46117
Ripe Pepper/Ripe Tomato	3.9679	0.256
Mature Eggplant/Ripe Tomato	0.84756	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06132	0.877
1-1-2/M82	1.07719	0.977
12-2/M82	N/A	N/A
12-4/M82	0.91884	1
1-3/M82	1.1031	0.479
2-1-1/M82	0.7743	0.465
2-1/M82	0.9435	0.74
2-6/M82	1.05411	1
3-2/M82	1.30174
4-1-1/M82	0.89441	1
4-1/M82	0.81895
4-3-2/M82	0.95132
4-3/M82	0.91815	1
5-3/M82	1.02966	1
6-2/M82	0.74037
6-3/M82	1.06266	1
7-1/M82	1.00529	1
7-2/M82	1.1196	1
9-3-2/M82	1.17789

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71661	0.243
IL2-6/WTpooled	1.31311	0.409
IL7-5/WTpooled	0.59414	1
IL7-3/WTpooled	0.72249	0.298
IL12-4/WTpooled	0.90009	0.581
IL1-4/WTpooled	0.92923	0.562
WT/WTpooled	1.06421	0.87

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	0.85295	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01079	1
DC3000/delta hrp 6h	1.0004	0.95
DC3000/delta hrp 12h	0.85418	1
DC3000/delta hrp 24h	0.76098	0.041

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56643	0.036
DC3000 delta B/DC3000 delta AB	0.73149	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8033	1
Exp 36h	0.66968	0.434
Exp 60h	0.5211	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02743	1
Var 0h	1.49679	0.936
Var 12h I row2-row1	0.76425	0.338
Var 12h NI row2-row1	0.99808	1
Var 36h I row2-row1	0.99027	1
Var 36h NI row2-row1	1.28309	1
Var 60h I row2-row1	0.90364	0.306
Var 60h NI row2-row1	1.19785	0.904
Time course 0hI-0hNI	0.87864	0.256
Time course 12hI-12hNI	1.04926	0.611
Time course 36hI-36hNI	0.89516	0.084
Time course 60hI-60hNI	0.19427	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)	1.08367	0.297
transgenic ySAMdc/azygous control (breaker)	1.11808	1
transgenic ySAMdc/azygous control (red)	1.10335	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.943	0.208

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.47323	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.19492	0.083
Manapal/WT (break)	2.05636	0.14
Manapal/WT (red)	2.60918	0.125