Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.9.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	58.3758	0.01
27DAP/17DAP	1.17353	0.88
39DAP/27DAP	0.93918	0.663
41DAP/39DAP	0.44899	0.041
42DAP/41DAP	0.62561	0.774
43DAP/42DAP	0.66744	0.554
47DAP/43DAP	1.37659	0.595
52DAP/47DAP	1.18706	0.994
57DAP/52DAP	1.76596	0.652

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5888	0.045
17DAP/reference	5.36186	0.013
27DAP/reference	5.59866	0.007
39DAP/reference	2.3692	0.029
41DAP/reference	2.6805	0.012
42DAP/reference	1.33437	0.001
43DAP/reference	0.92695	0.346
47DAP/reference	0.94259	0.161
52DAP/reference	1.27487	0.102
57DAP/reference	1.22646	0.052

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	6.29995	0.047
27DAP/17DAP	1.40759	0.119
39DAP/27DAP	0.53101	0.03
41DAP/39DAP	0.99696	0.91
42DAP/41DAP	0.97968	0.715
43DAP/42DAP	0.3698	0.02
47DAP/43DAP	0.67847	0.008
52DAP/47DAP	1.681	0.096
57DAP/52DAP	1.0154	0.862
57DAP/7DAP	1.16088	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.112	1
17DAP/reference	5.24234	0.006
27DAP/reference	4.20047	0.006
39DAP/reference	3.24372	0.005
41DAP/reference	1.9577	0.008
42DAP/reference	1.30015	0.405
43DAP/reference	0.64545	0.016
47DAP/reference	1.1194	0.582
52DAP/reference	0.68839	0.012
57DAP/reference	0.66864	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.39488	0.007
17DAP/reference	5.54175	0.007
27DAP/reference	4.89099	0.012
39DAP/reference	4.08309	0.011
41DAP/reference	2.43314	0.014
42DAP/reference	2.78896	0.008
43DAP/reference	3.03583	0.021
47DAP/reference	1.55043	0.065
52DAP/reference	4.13585	0.006
57DAP/reference	1.24963	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.50805	0.057
17DAP/reference	1.52952	0.092
27DAP/reference	3.89319	0.008
39DAP/reference	2.2258	0.009
41DAP/reference	1.4427	0.009
42DAP/reference	0.95702	0.552
43DAP/reference	0.70535	0.035
47DAP/reference	0.56846	0.005
52DAP/reference	0.61611	0.058
57DAP/reference	1.74796	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87032	1
26DAP/20DAP	0.75454	0.244
34DAP/26DAP	1.38126	0.19
51DAP/34DAP	1.59411	0.067
52DAP/51DAP	0.87338	1
53DAP/52DAP	3.22169	0.021
55DAP/53DAP	1.16504	0.375
57DAP/55DAP	0.97284	0.78
62DAP/57DAP	0.78672	0.28
68DAP/62DAP	0.87303	0.464
68DAP/14DAP	1.3132	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.23261	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.20914	0.059
Mature Green Tomato/Ripe Tomato	5.45	0.016
Immature Eggplant/Mature Eggplant	18.0804	0.05
Ripe Pepper/Ripe Tomato	0.11187	0.224
Mature Eggplant/Ripe Tomato	0.21906	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.49473	0.651
1-1-2/M82	1.1331	1
12-2/M82	1.29802	1
12-4/M82	0.84776	0.619
1-3/M82	2.9961	0.26
2-1-1/M82	1.02238	1
2-1/M82	1.05672	1
2-6/M82	0.77172	1
3-2/M82	1.83442	0.549
4-1-1/M82	1.49958	1
4-1/M82	1.28943	N/A
4-3-2/M82	0.58966	0.487
4-3/M82	0.80382	0.578
5-3/M82	1.26555	1
6-2/M82	0.91277	1
6-3/M82	1.18297	1
7-1/M82	1.21589	0.598
7-2/M82	1.06583	1
9-3-2/M82	0.81466	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9213	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.97326	N/A
WT/WTpooled	N/A	N/A

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	0.87685	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13625	0.656
DC3000/delta hrp 6h	0.9925	0.95
DC3000/delta hrp 12h	1.18934	1
DC3000/delta hrp 24h	0.39342	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87371	0.538
DC3000 delta B/DC3000 delta AB	0.86094	0.041

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84698	1
Exp 36h	0.43668	0.406
Exp 60h	0.32587	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0197	1
Var 0h	0.59761	0.311
Var 12h I row2-row1	0.77677	0.565
Var 12h NI row2-row1	0.84167	0.713
Var 36h I row2-row1	1.12028	1
Var 36h NI row2-row1	1.58954	0.276
Var 60h I row2-row1	1.24187	0.562
Var 60h NI row2-row1	0.96279	1
Time course 0hI-0hNI	1.08665	0.719
Time course 12hI-12hNI	0.87331	0.228
Time course 36hI-36hNI	0.58584	0.023
Time course 60hI-60hNI	0.05519	0.005

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)	1.02987	0.921
transgenic ySAMdc/azygous control (breaker)	1.17574	1
transgenic ySAMdc/azygous control (red)	0.83346	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.8804	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03039	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67072	1
Manapal/WT (break)	0.22971	0.285
Manapal/WT (red)	0.7645	0.274