Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04274	0.919
27DAP/17DAP	1.0372	1
39DAP/27DAP	0.92196	0.652
41DAP/39DAP	0.88536	0.527
42DAP/41DAP	1.23603	0.841
43DAP/42DAP	0.94421	0.877
47DAP/43DAP	1.09562	0.668
52DAP/47DAP	1.0767	0.991
57DAP/52DAP	1.35403	0.652

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83381	0.098
17DAP/reference	0.87311	0.097
27DAP/reference	0.87062	0.065
39DAP/reference	1.022	0.771
41DAP/reference	0.75985	0.018
42DAP/reference	0.9232	0.041
43DAP/reference	0.95586	0.611
47DAP/reference	1.35464	0.002
52DAP/reference	1.1559	0.176
57DAP/reference	1.16757	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02858	0.923
27DAP/17DAP	1.3797	0.088
39DAP/27DAP	1.00802	1
41DAP/39DAP	1.06175	0.883
42DAP/41DAP	1.00675	0.892
43DAP/42DAP	1.08149	0.351
47DAP/43DAP	1.12527	0.471
52DAP/47DAP	0.7697	0.164
57DAP/52DAP	0.91929	0.461
57DAP/7DAP	0.82704	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18695	0.193
17DAP/reference	1.08187	0.399
27DAP/reference	1.10846	0.371
39DAP/reference	0.97885	0.474
41DAP/reference	1.00399	0.741
42DAP/reference	1.20653	0.405
43DAP/reference	1.104	0.569
47DAP/reference	1.12545	0.44
52DAP/reference	1.13896	0.375
57DAP/reference	0.97317	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01835	0.951
17DAP/reference	0.91871	0.347
27DAP/reference	0.99809	0.642
39DAP/reference	0.95128	0.455
41DAP/reference	0.95158	0.322
42DAP/reference	0.90711	0.261
43DAP/reference	0.85424	0.092
47DAP/reference	1.06631	0.454
52DAP/reference	0.86434	0.014
57DAP/reference	0.8144	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08584	0.882
17DAP/reference	0.92695	0.313
27DAP/reference	3.77213	0.357
39DAP/reference	0.97018	0.544
41DAP/reference	0.80081	0.132
42DAP/reference	1.13683	0.671
43DAP/reference	1.01717	0.767
47DAP/reference	1.00061	0.731
52DAP/reference	1.49908	0.148
57DAP/reference	1.21746	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10853	0.966
26DAP/20DAP	1.07128	0.855
34DAP/26DAP	1.08117	1
51DAP/34DAP	1.27462	0.118
52DAP/51DAP	0.72868	0.151
53DAP/52DAP	1.43668	0.384
55DAP/53DAP	0.97061	0.784
57DAP/55DAP	1.2617	0.474
62DAP/57DAP	0.83928	0.28
68DAP/62DAP	0.86303	0.579
68DAP/14DAP	1.19773	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08241	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0393	1
Mature Green Tomato/Ripe Tomato	0.47459	0.042
Immature Eggplant/Mature Eggplant	1.65885
Ripe Pepper/Ripe Tomato	0.85598	0.293
Mature Eggplant/Ripe Tomato	0.5197	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9053	0.944
1-1-2/M82	1.19729	0.977
12-2/M82	0.64531
12-4/M82	0.90044	1
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	0.90395	1
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	1.10333
5-3/M82	1.1097	1
6-2/M82	0.97519
6-3/M82	1.02607	1
7-1/M82	N/A	N/A
7-2/M82	1.01572
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09269	0.277
IL2-6/WTpooled	0.95271	1
IL7-5/WTpooled	1.07496	1
IL7-3/WTpooled	0.99358	1
IL12-4/WTpooled	0.88213	0.71
IL1-4/WTpooled	0.84571	0.402
WT/WTpooled	0.94497	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	0.97726	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0575	0.914
DC3000/delta hrp 6h	0.99942	0.95
DC3000/delta hrp 12h	1.04677	1
DC3000/delta hrp 24h	1.0324	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.03857
DC3000 delta B/DC3000 delta AB	0.84145	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.07489	1
Exp 60h	0.90418	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1168	1
Var 0h	1.02115	1
Var 12h I row2-row1	1.00051	1
Var 12h NI row2-row1	1.06094	1
Var 36h I row2-row1	0.8755	1
Var 36h NI row2-row1	1.13107	1
Var 60h I row2-row1	0.9288	0.952
Var 60h NI row2-row1	0.97611	1
Time course 0hI-0hNI	0.97202	0.839
Time course 12hI-12hNI	1.05888	0.554
Time course 36hI-36hNI	1.01929	1
Time course 60hI-60hNI	1.12843	0.025

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)	0.97925	0.662
transgenic ySAMdc/azygous control (breaker)	1.14912	0.248
transgenic ySAMdc/azygous control (red)	0.89204	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95115	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93121	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94472	1
Manapal/WT (break)	0.73399	0.333
Manapal/WT (red)	0.89996	0.36