Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.18.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1983	0.656
27DAP/17DAP	1.26691	0.836
39DAP/27DAP	0.98053	0.769
41DAP/39DAP	0.98047	0.876
42DAP/41DAP	1.1798	0.825
43DAP/42DAP	1.23443	0.867
47DAP/43DAP	1.36609	0.668
52DAP/47DAP	0.69633	0.216
57DAP/52DAP	0.94084	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95725	0.455
17DAP/reference	1.0164	0.787
27DAP/reference	0.96052	0.514
39DAP/reference	0.96612	0.611
41DAP/reference	0.90583	0.201
42DAP/reference	0.93926	0.124
43DAP/reference	0.96697	0.611
47DAP/reference	0.9433	0.207
52DAP/reference	0.99398	0.654
57DAP/reference	0.91492	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99831	0.629
27DAP/17DAP	1.06234	0.969
39DAP/27DAP	1.08097	0.707
41DAP/39DAP	0.96671	0.997
42DAP/41DAP	0.95379	0.662
43DAP/42DAP	1.27281	0.052
47DAP/43DAP	0.99291	0.983
52DAP/47DAP	1.15057	0.927
57DAP/52DAP	1.47002	0.215
57DAP/7DAP	2.4222

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33513	0.091
17DAP/reference	1.59091	0.084
27DAP/reference	1.57475	0.007
39DAP/reference	1.45684	0.008
41DAP/reference	1.45587	0.117
42DAP/reference	1.65138	0.008
43DAP/reference	1.58852	0.009
47DAP/reference	1.29536	0.413
52DAP/reference	1.54316	0.008
57DAP/reference	1.64961	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9126	0.412
17DAP/reference	0.89268	0.26
27DAP/reference	0.88678	0.144
39DAP/reference	1.14634	0.424
41DAP/reference	0.92765	0.188
42DAP/reference	0.84745	0.03
43DAP/reference	0.99423	0.657
47DAP/reference	0.9633	0.319
52DAP/reference	1.00712	1
57DAP/reference	1.11951	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28646	0.069
17DAP/reference	0.9042	0.364
27DAP/reference	1.39124	0.021
39DAP/reference	1.31803	0.013
41DAP/reference	1.17548	0.15
42DAP/reference	1.16263	0.47
43DAP/reference	1.15902	0.474
47DAP/reference	0.9965	0.626
52DAP/reference	1.19312	0.463
57DAP/reference	1.01736	0.888

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.63326	0.878
26DAP/20DAP	0.95721	1
34DAP/26DAP	0.42538	0.076
51DAP/34DAP	0.93597
52DAP/51DAP	1.73922	0.534
53DAP/52DAP	1.01245	1
55DAP/53DAP	1.05139	1
57DAP/55DAP	0.99418	0.93
62DAP/57DAP	0.93761	0.871
68DAP/62DAP	0.76976	0.211
68DAP/14DAP	0.71526	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69989	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.32471	0.399
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.0134
Mature Eggplant/Ripe Tomato	1.09723

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00924	1
1-1-2/M82	0.93985	0.804
12-2/M82	1.04946	1
12-4/M82	1.03034	1
1-3/M82	0.89465	0.378
2-1-1/M82	1.41826
2-1/M82	1.34753	0.345
2-6/M82	1.32017	0.425
3-2/M82	0.98517
4-1-1/M82	1.03287	1
4-1/M82	0.95384
4-3-2/M82	1.0386
4-3/M82	0.87205	1
5-3/M82	0.99202	1
6-2/M82	1.06548	1
6-3/M82	0.98334	1
7-1/M82	0.92867
7-2/M82	1.06792	1
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	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	N/A	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	1.01505	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9796	1
DC3000/delta hrp 6h	2.43255	1
DC3000/delta hrp 12h	1.12451	1
DC3000/delta hrp 24h	1.05764	0.69

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	1.08071	1
Exp 36h	N/A	N/A
Exp 60h	1.35561	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11301	1
Var 0h	0.98012	1
Var 12h I row2-row1	0.93227	0.856
Var 12h NI row2-row1	1.55735	1
Var 36h I row2-row1	0.93781	1
Var 36h NI row2-row1	0.69243	0.645
Var 60h I row2-row1	0.98867	1
Var 60h NI row2-row1	1.1545	1
Time course 0hI-0hNI	1.28872	0.799
Time course 12hI-12hNI	0.77753	0.698
Time course 36hI-36hNI	0.94724	0.433
Time course 60hI-60hNI	4.51183	0.16

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)	0.96359	0.614
transgenic ySAMdc/azygous control (breaker)	1.25429	0.178
transgenic ySAMdc/azygous control (red)	0.71886	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96969	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94847	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92113	1
Manapal/WT (break)	0.81173	0.333
Manapal/WT (red)	1.00275	1