Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16687	0.602
27DAP/17DAP	1.1715	0.859
39DAP/27DAP	1.25609	0.649
41DAP/39DAP	0.94545	0.717
42DAP/41DAP	1.20155	0.712
43DAP/42DAP	1.12814	0.999
47DAP/43DAP	1.11478	0.842
52DAP/47DAP	1.25404	0.702
57DAP/52DAP	1.2436	0.524

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90954	0.068
17DAP/reference	0.95191	0.12
27DAP/reference	1.01415	0.735
39DAP/reference	0.98367	0.691
41DAP/reference	0.99627	1
42DAP/reference	0.98228	0.315
43DAP/reference	1.00963	0.957
47DAP/reference	0.97277	0.098
52DAP/reference	0.96363	0.319
57DAP/reference	1.11327	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02815	0.65
27DAP/17DAP	0.96887	0.748
39DAP/27DAP	1.01062	0.799
41DAP/39DAP	1.06038	0.663
42DAP/41DAP	0.99824	0.907
43DAP/42DAP	0.97859	0.576
47DAP/43DAP	0.99968	1
52DAP/47DAP	0.98424	0.919
57DAP/52DAP	1.02146	0.906
57DAP/7DAP	1.03073	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94021	0.039
17DAP/reference	1.02577	0.477
27DAP/reference	1.03926	0.246
39DAP/reference	1.07025	0.01
41DAP/reference	1.0648	0.363
42DAP/reference	1.07016	0.132
43DAP/reference	1.0823	0.118
47DAP/reference	1.09972	0.165
52DAP/reference	1.00723	1
57DAP/reference	1.09274	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01203	0.787
17DAP/reference	1.02702	0.658
27DAP/reference	0.98161	0.483
39DAP/reference	0.95132	0.165
41DAP/reference	0.95155	0.194
42DAP/reference	1.00275	1
43DAP/reference	0.96182	0.352
47DAP/reference	1.07043	0.148
52DAP/reference	0.91804	0.029
57DAP/reference	1.00872	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98392	0.653
17DAP/reference	0.97464	0.668
27DAP/reference	1.06844	0.357
39DAP/reference	0.95129	0.591
41DAP/reference	1.041	0.369
42DAP/reference	1.08028	0.258
43DAP/reference	1.00528	1
47DAP/reference	0.92618	0.109
52DAP/reference	1.03149	0.694
57DAP/reference	1.08389	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02616	0.966
26DAP/20DAP	0.97899	1
34DAP/26DAP	0.91926	0.364
51DAP/34DAP	1.03999	0.795
52DAP/51DAP	0.98858	1
53DAP/52DAP	0.96156	0.767
55DAP/53DAP	0.97318	0.807
57DAP/55DAP	1.02238	1
62DAP/57DAP	0.91251	0.028
68DAP/62DAP	1.18696	0.107
68DAP/14DAP	1.08065	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0629	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07269	0.287
Mature Green Tomato/Ripe Tomato	1.4527	0.053
Immature Eggplant/Mature Eggplant	1.39423	0.05
Ripe Pepper/Ripe Tomato	0.86149	1
Mature Eggplant/Ripe Tomato	1.00928	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03384	1
1-1-2/M82	1.07493	1
12-2/M82	1.01405	1
12-4/M82	1.05596	1
1-3/M82	0.98233	1
2-1-1/M82	0.85662	0.683
2-1/M82	1.0784	1
2-6/M82	0.91014	1
3-2/M82	0.99427	1
4-1-1/M82	0.9886	1
4-1/M82	1.1154	1
4-3-2/M82	1.11882	0.262
4-3/M82	0.9983	1
5-3/M82	0.99055	1
6-2/M82	1.05242	1
6-3/M82	1.01766	1
7-1/M82	1.0102	1
7-2/M82	1.05049	1
9-3-2/M82	1.11137	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89173	1
IL12-4/WTpooled	1.04536	1
IL1-4/WTpooled	1.02871	1
WT/WTpooled	0.92341	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	1.05889	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08357	0.921
DC3000/delta hrp 6h	0.90717	0.95
DC3000/delta hrp 12h	0.98877	1
DC3000/delta hrp 24h	0.96379	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01558	0.598
DC3000 delta B/DC3000 delta AB	1.10006	0.368

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.31166	1
Exp 36h	0.9268	0.82
Exp 60h	1.01195	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00878	1
Var 0h	0.97915	1
Var 12h I row2-row1	1.21714	0.224
Var 12h NI row2-row1	1.01374	1
Var 36h I row2-row1	1.35801	1
Var 36h NI row2-row1	0.80596	0.61
Var 60h I row2-row1	1.00668	1
Var 60h NI row2-row1	1.09585	1
Time course 0hI-0hNI	1.05847	0.852
Time course 12hI-12hNI	1.07617	0.517
Time course 36hI-36hNI	0.9648	0.484
Time course 60hI-60hNI	1.4766	0.01

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)	0.8337	0.314
transgenic ySAMdc/azygous control (breaker)	0.94264	1
transgenic ySAMdc/azygous control (red)	1.21925	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05357	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89745	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00699	1
Manapal/WT (break)	0.81894	0.333
Manapal/WT (red)	1.05932	1