Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.15.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05409	0.851
27DAP/17DAP	1.03336	0.926
39DAP/27DAP	0.94626	0.663
41DAP/39DAP	1.25596	0.217
42DAP/41DAP	0.97987	1
43DAP/42DAP	0.95253	0.888
47DAP/43DAP	1.0537	0.569
52DAP/47DAP	0.96218	0.875
57DAP/52DAP	0.99187	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94142	0.172
17DAP/reference	0.92792	0.085
27DAP/reference	0.95788	0.215
39DAP/reference	0.95413	0.412
41DAP/reference	0.90644	0.114
42DAP/reference	0.88542	0.003
43DAP/reference	0.94917	0.17
47DAP/reference	0.98653	0.503
52DAP/reference	1.05644	0.186
57DAP/reference	0.97828	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9994	0.899
27DAP/17DAP	1.02055	0.928
39DAP/27DAP	0.97815	0.821
41DAP/39DAP	0.97372	0.885
42DAP/41DAP	1.0308	0.879
43DAP/42DAP	1.03235	0.147
47DAP/43DAP	0.97316	0.833
52DAP/47DAP	0.95953	0.726
57DAP/52DAP	0.97748	0.637
57DAP/7DAP	0.96842	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85368	0.076
17DAP/reference	1.01036	0.971
27DAP/reference	0.94952	0.117
39DAP/reference	1.02473	0.436
41DAP/reference	0.98195	0.449
42DAP/reference	1.0203	1
43DAP/reference	1.08928	0.093
47DAP/reference	1.10724	0.318
52DAP/reference	0.97352	0.477
57DAP/reference	0.98376	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96683	0.532
17DAP/reference	0.86535	0.009
27DAP/reference	0.92967	0.181
39DAP/reference	0.92121	0.097
41DAP/reference	0.89127	0.112
42DAP/reference	0.93066	0.089
43DAP/reference	0.89699	0.049
47DAP/reference	0.98465	0.512
52DAP/reference	0.91338	0.011
57DAP/reference	0.89262	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87439	0.031
17DAP/reference	0.94782	0.249
27DAP/reference	0.92831	0.036
39DAP/reference	0.90026	0.029
41DAP/reference	0.9571	0.371
42DAP/reference	1.1868	0.078
43DAP/reference	1.10189	0.32
47DAP/reference	0.9486	0.174
52DAP/reference	1.14827	0.405
57DAP/reference	1.02037	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04147	0.966
26DAP/20DAP	0.96502	0.512
34DAP/26DAP	0.98662	0.998
51DAP/34DAP	1.04422	0.759
52DAP/51DAP	1.00188	0.965
53DAP/52DAP	0.96163	0.835
55DAP/53DAP	0.92889	0.619
57DAP/55DAP	0.9881	0.925
62DAP/57DAP	0.9741	0.994
68DAP/62DAP	1.04814	0.866
68DAP/14DAP	1.20068	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03299	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1353
Mature Green Tomato/Ripe Tomato	0.92845	0.446
Immature Eggplant/Mature Eggplant	1.22284	0.311
Ripe Pepper/Ripe Tomato	0.56803	1
Mature Eggplant/Ripe Tomato	0.76427	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98421	0.961
1-1-2/M82	0.94969	1
12-2/M82	1.14191	1
12-4/M82	0.91694	0.619
1-3/M82	0.9512	0.378
2-1-1/M82	0.99067	1
2-1/M82	1.17652	0.312
2-6/M82	0.95997	1
3-2/M82	0.90339	0.752
4-1-1/M82	1.03619	1
4-1/M82	1.14928	0.328
4-3-2/M82	0.99941	1
4-3/M82	1.08927	1
5-3/M82	1.02219	1
6-2/M82	0.98948	1
6-3/M82	0.97916	1
7-1/M82	1.08627	0.598
7-2/M82	1.05234	0.299
9-3-2/M82	0.92894	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17985	1
IL2-6/WTpooled	0.907	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.26232	1
IL12-4/WTpooled	0.97031	1
IL1-4/WTpooled	0.89287
WT/WTpooled	1.04876	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	0.79193	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0239	0.914
DC3000/delta hrp 6h	0.93069	0.95
DC3000/delta hrp 12h	0.95033	1
DC3000/delta hrp 24h	1.02409	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13344	0.042
DC3000 delta B/DC3000 delta AB	1.0557	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03156	1
Exp 36h	1.15402	0.693
Exp 60h	1.01163	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99193	1
Var 0h	1.07629	0.594
Var 12h I row2-row1	1.1556	0.296
Var 12h NI row2-row1	0.92739	0.546
Var 36h I row2-row1	1.07584	1
Var 36h NI row2-row1	0.87506	0.61
Var 60h I row2-row1	1.42363	0.562
Var 60h NI row2-row1	1.10688	0.904
Time course 0hI-0hNI	1.0532	0.852
Time course 12hI-12hNI	1.03739	0.724
Time course 36hI-36hNI	0.96423	0.403
Time course 60hI-60hNI	1.02794	0.495

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)	0.94585	0.529
transgenic ySAMdc/azygous control (breaker)	0.87874	0.49
transgenic ySAMdc/azygous control (red)	1.03289	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01434	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05923	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87819	1
Manapal/WT (break)	0.99344	1
Manapal/WT (red)	1.15819	0.15