Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99084	0.77
27DAP/17DAP	1.22753	0.761
39DAP/27DAP	1.09402	0.894
41DAP/39DAP	1.06486	0.905
42DAP/41DAP	1.08315	1
43DAP/42DAP	1.05324	1
47DAP/43DAP	1.17863	0.756
52DAP/47DAP	1.00244	0.783
57DAP/52DAP	1.00869	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95154	0.442
17DAP/reference	1.09371	0.154
27DAP/reference	1.01423	0.847
39DAP/reference	1.04833	0.557
41DAP/reference	1.0829	0.451
42DAP/reference	0.89982	0.048
43DAP/reference	0.94098	0.394
47DAP/reference	0.9311	0.06
52DAP/reference	0.90471	0.258
57DAP/reference	0.78577	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03892	0.841
27DAP/17DAP	0.96116	0.854
39DAP/27DAP	1.13572	0.534
41DAP/39DAP	0.9848	1
42DAP/41DAP	0.98475	0.795
43DAP/42DAP	0.8997	0.576
47DAP/43DAP	0.85578	0.418
52DAP/47DAP	0.92102	0.612
57DAP/52DAP	0.91842	0.626
57DAP/7DAP	1.18713	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05636	1
17DAP/reference	0.85647	0.144
27DAP/reference	0.89717	0.159
39DAP/reference	1.08005	0.669
41DAP/reference	0.96748	0.489
42DAP/reference	1.02169	1
43DAP/reference	0.78526	0.095
47DAP/reference	0.81397	0.168
52DAP/reference	1.03458	0.679
57DAP/reference	1.00885	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99463	0.884
17DAP/reference	0.89022	0.106
27DAP/reference	0.82916	0.032
39DAP/reference	0.87694	0.235
41DAP/reference	0.75153	0.027
42DAP/reference	0.83518	0.039
43DAP/reference	0.93991	0.385
47DAP/reference	0.93864	0.159
52DAP/reference	0.94868	0.239
57DAP/reference	1.12186	0.324

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04103	1
17DAP/reference	0.95054	0.56
27DAP/reference	0.84092	0.063
39DAP/reference	0.89571	0.246
41DAP/reference	1.06212	0.84
42DAP/reference	1.25878	0.627
43DAP/reference	0.8687	0.267
47DAP/reference	0.96376	0.452
52DAP/reference	1.68398	0.457
57DAP/reference	0.63262	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10214	0.966
26DAP/20DAP	1.27726
34DAP/26DAP	1.00335	1
51DAP/34DAP	1.24881	0.795
52DAP/51DAP	1.24974	0.783
53DAP/52DAP	0.70144	0.086
55DAP/53DAP	1.19362	0.645
57DAP/55DAP	0.85608	0.391
62DAP/57DAP	1.13693	0.833
68DAP/62DAP	0.91061	0.722
68DAP/14DAP	0.98967	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89644	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06237
Mature Green Tomato/Ripe Tomato	1.36495	0.028
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.33503
Mature Eggplant/Ripe Tomato	0.84093	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.6506
12-2/M82	N/A	N/A
12-4/M82	0.79759	0.619
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	N/A	N/A
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	1.05663	0.232
4-3/M82	1.10834	1
5-3/M82	1.07078	1
6-2/M82	N/A	N/A
6-3/M82	0.89551
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.0876	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.9527	1
IL7-5/WTpooled	1.16551
IL7-3/WTpooled	0.88884	0.31
IL12-4/WTpooled	1.28673	0.538
IL1-4/WTpooled	0.86598	0.415
WT/WTpooled	1.02964	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	0.71288	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.23286
DC3000/delta hrp 6h	0.70827	0.95
DC3000/delta hrp 12h	0.92983	1
DC3000/delta hrp 24h	0.97585	0.957

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00073	1
Exp 36h	0.93809	0.699
Exp 60h	0.93937	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08784	1
Var 0h	0.87721	0.457
Var 12h I row2-row1	0.85155	0.39
Var 12h NI row2-row1	1.03372	1
Var 36h I row2-row1	0.86073	1
Var 36h NI row2-row1	0.8411	0.645
Var 60h I row2-row1	0.98129	0.832
Var 60h NI row2-row1	0.96959	1
Time course 0hI-0hNI	0.95499	0.659
Time course 12hI-12hNI	0.9485	0.782
Time course 36hI-36hNI	0.98663	0.632
Time course 60hI-60hNI	0.94032	0.646

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)	0.97747	0.409
transgenic ySAMdc/azygous control (breaker)	0.9644	0.49
transgenic ySAMdc/azygous control (red)	0.99757	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99967	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96903	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90227	1
Manapal/WT (break)	1.01191	1
Manapal/WT (red)	1.07468	0.413