Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80712	0.26
27DAP/17DAP	1.1262	0.905
39DAP/27DAP	1.86844	0.107
41DAP/39DAP	0.79561	0.291
42DAP/41DAP	1.43781	0.514
43DAP/42DAP	1.10723	1
47DAP/43DAP	0.92962	0.701
52DAP/47DAP	1.27813	0.943
57DAP/52DAP	1.22385	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00646	1
17DAP/reference	0.87472	0.009
27DAP/reference	0.9514	0.257
39DAP/reference	1.06891	0.301
41DAP/reference	0.93468	0.267
42DAP/reference	1.03991	0.352
43DAP/reference	1.01091	0.957
47DAP/reference	1.00923	1
52DAP/reference	1.21027	0.024
57DAP/reference	1.13654	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94056	0.595
27DAP/17DAP	0.97379	0.887
39DAP/27DAP	1.07551	0.534
41DAP/39DAP	1.00906	0.959
42DAP/41DAP	1.17044	0.47
43DAP/42DAP	1.00663	1
47DAP/43DAP	1.01082	0.963
52DAP/47DAP	0.92704	0.694
57DAP/52DAP	1.02087	0.978
57DAP/7DAP	0.86496	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43581	0.035
17DAP/reference	1.11433	0.297
27DAP/reference	1.17248	0.197
39DAP/reference	1.09616	0.411
41DAP/reference	1.09134	0.678
42DAP/reference	0.93495	0.338
43DAP/reference	1.10891	0.386
47DAP/reference	1.123	0.421
52DAP/reference	1.33432	0.015
57DAP/reference	1.32877	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05406	0.724
17DAP/reference	0.98483	0.611
27DAP/reference	1.10854	0.497
39DAP/reference	1.1704	0.164
41DAP/reference	0.9879	0.545
42DAP/reference	1.06182	0.408
43DAP/reference	0.95579	0.468
47DAP/reference	1.01195	0.965
52DAP/reference	0.91623	0.021
57DAP/reference	0.87772	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0407	0.676
17DAP/reference	0.99507	0.792
27DAP/reference	0.85972	0.039
39DAP/reference	1.11958	0.03
41DAP/reference	1.28951	0.086
42DAP/reference	1.31272	0.034
43DAP/reference	1.23877	0.066
47DAP/reference	1.00678	1
52DAP/reference	1.13708	0.335
57DAP/reference	1.42347	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31743	0.966
26DAP/20DAP	1.93839	0.097
34DAP/26DAP	0.98395	0.988
51DAP/34DAP	1.22235	0.164
52DAP/51DAP	0.89952	1
53DAP/52DAP	0.96771	0.844
55DAP/53DAP	0.7771	0.125
57DAP/55DAP	1.28025	0.311
62DAP/57DAP	0.89519	0.162
68DAP/62DAP	1.22773	0.885
68DAP/14DAP	1.03768	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20467	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26136	0.063
Mature Green Tomato/Ripe Tomato	1.10632	0.752
Immature Eggplant/Mature Eggplant	1.57369	0.05
Ripe Pepper/Ripe Tomato	0.37684	0.224
Mature Eggplant/Ripe Tomato	0.72036	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.21149	1
1-3/M82	N/A	N/A
2-1-1/M82	0.87217
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.15737
4-1-1/M82	N/A	N/A
4-1/M82	1.86477
4-3-2/M82	0.92015	1
4-3/M82	N/A	N/A
5-3/M82	1.45003
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.97977
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.92574	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88214	1
IL12-4/WTpooled	1.1221	0.523
IL1-4/WTpooled	1.05371	1
WT/WTpooled	0.93945	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	1.19423	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17657	0.875
DC3000/delta hrp 6h	1.03813	1
DC3000/delta hrp 12h	0.97297	1
DC3000/delta hrp 24h	1.03895	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32242	0.045
DC3000 delta B/DC3000 delta AB	1.20821	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91922	1
Exp 36h	1.00895	1
Exp 60h	0.98356	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97594	1
Var 0h	1.05669	0.98
Var 12h I row2-row1	1.17515	0.58
Var 12h NI row2-row1	1.21486	0.649
Var 36h I row2-row1	1.19067	0.489
Var 36h NI row2-row1	0.9573	0.791
Var 60h I row2-row1	0.85406	0.582
Var 60h NI row2-row1	0.90085	0.818
Time course 0hI-0hNI	0.90834	0.309
Time course 12hI-12hNI	1.02185	0.803
Time course 36hI-36hNI	1.39644	0.01
Time course 60hI-60hNI	1.59005	0.009

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)	1.0591	0.408
transgenic ySAMdc/azygous control (breaker)	0.89191	0.251
transgenic ySAMdc/azygous control (red)	1.11852	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92798	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.39769	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94623	1
Manapal/WT (break)	0.95552	1
Manapal/WT (red)	1.36954	0.222