Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07533	0.961
27DAP/17DAP	1.8077	0.606
39DAP/27DAP	0.99264	0.82
41DAP/39DAP	0.92159	0.743
42DAP/41DAP	0.7665	1
43DAP/42DAP	0.80537	0.743
47DAP/43DAP	0.89162	0.625
52DAP/47DAP	1.28749	0.844
57DAP/52DAP	1.24084	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13212	0.197
17DAP/reference	1.03013	0.33
27DAP/reference	0.95736	0.187
39DAP/reference	1.00801	0.842
41DAP/reference	0.99576	1
42DAP/reference	1.07997	0.084
43DAP/reference	0.99742	0.904
47DAP/reference	1.03297	0.448
52DAP/reference	0.9789	0.504
57DAP/reference	1.02161	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.89104	0.719
27DAP/17DAP	0.83652	0.58
39DAP/27DAP	0.8875	0.55
41DAP/39DAP	1.32054	0.531
42DAP/41DAP	0.74859	0.161
43DAP/42DAP	1.12251	0.664
47DAP/43DAP	1.40554	0.444
52DAP/47DAP	1.38236	0.308
57DAP/52DAP	1.30922	0.596
57DAP/7DAP	0.97063

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37526	0.043
17DAP/reference	1.90855	0.008
27DAP/reference	1.88535	0.006
39DAP/reference	2.35702	0.006
41DAP/reference	2.3474	0.01
42DAP/reference	3.01103	0.006
43DAP/reference	2.66521	0.006
47DAP/reference	1.5241	0.161
52DAP/reference	1.9341	0.007
57DAP/reference	1.94633	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06977	0.484
17DAP/reference	1.14392	0.032
27DAP/reference	1.14187	0.174
39DAP/reference	1.1007	0.281
41DAP/reference	1.05282	0.925
42DAP/reference	1.02433	1
43DAP/reference	1.0675	0.777
47DAP/reference	1.028	0.965
52DAP/reference	1.03006	0.444
57DAP/reference	1.16608	0.048

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48075	0.028
17DAP/reference	1.23203	0.321
27DAP/reference	1.46337	0.022
39DAP/reference	1.50337	0.014
41DAP/reference	1.54911	0.018
42DAP/reference	1.33958	0.028
43DAP/reference	1.62196	0.011
47DAP/reference	0.95925	0.335
52DAP/reference	1.7688	0.056
57DAP/reference	1.3188	0.274

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.90048	0.966
26DAP/20DAP	1.68868	0.357
34DAP/26DAP	0.99186	1
51DAP/34DAP	1.33184	0.927
52DAP/51DAP	0.83658	1
53DAP/52DAP	0.58527	0.068
55DAP/53DAP	0.95028	0.735
57DAP/55DAP	1.19015	0.865
62DAP/57DAP	0.82005	0.28
68DAP/62DAP	0.959	0.81
68DAP/14DAP	0.5428	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69369	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9143	0.491
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.57849	0.05
Ripe Pepper/Ripe Tomato	0.98003	1
Mature Eggplant/Ripe Tomato	0.655	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94653	0.944
1-1-2/M82	1.15982	1
12-2/M82	1.00625	1
12-4/M82	0.9728	1
1-3/M82	0.75565	1
2-1-1/M82	1.03261	1
2-1/M82	0.95469	0.519
2-6/M82	1.0784	0.695
3-2/M82	0.88635
4-1-1/M82	1.03659	1
4-1/M82	1.32493
4-3-2/M82	1.53362
4-3/M82	1.41955	0.268
5-3/M82	1.13109	1
6-2/M82	N/A	N/A
6-3/M82	0.70687
7-1/M82	0.92656	0.803
7-2/M82	1.01498	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95382	1
IL2-6/WTpooled	1.01511	1
IL7-5/WTpooled	0.54158
IL7-3/WTpooled	1.19881	0.362
IL12-4/WTpooled	1.06373	0.737
IL1-4/WTpooled	1.20897	1
WT/WTpooled	0.97133	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	1.04242	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1108	0.692
DC3000/delta hrp 6h	0.99448	0.95
DC3000/delta hrp 12h	1.04277	1
DC3000/delta hrp 24h	1.05812	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1283	0.16
DC3000 delta B/DC3000 delta AB	1.17189	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96627	1
Exp 36h	1.23038	0.693
Exp 60h	1.01282	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97472	1
Var 0h	0.90242	0.933
Var 12h I row2-row1	0.99781	1
Var 12h NI row2-row1	0.90588	0.906
Var 36h I row2-row1	1.23552	0.298
Var 36h NI row2-row1	1.92644	0.791
Var 60h I row2-row1	0.81298	0.374
Var 60h NI row2-row1	0.95091	1
Time course 0hI-0hNI	1.10548	0.537
Time course 12hI-12hNI	1.07787	0.381
Time course 36hI-36hNI	1.35829	0.008
Time course 60hI-60hNI	1.83063	0.008

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)	1.02411	0.612
transgenic ySAMdc/azygous control (breaker)	1.10971	1
transgenic ySAMdc/azygous control (red)	1.1318	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08438	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93633	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91263	1
Manapal/WT (break)	1.21805	1
Manapal/WT (red)	1.22931	0.222