Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.15.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09447	0.851
27DAP/17DAP	1.17325	0.849
39DAP/27DAP	1.09826	1
41DAP/39DAP	0.95982	0.839
42DAP/41DAP	1.13198	0.945
43DAP/42DAP	1.09913	1
47DAP/43DAP	1.03115	0.98
52DAP/47DAP	0.86853	0.639
57DAP/52DAP	1.13605	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0132	0.96
17DAP/reference	1.0399	0.122
27DAP/reference	0.99046	0.725
39DAP/reference	1.04449	0.294
41DAP/reference	1.08297	0.047
42DAP/reference	1.00797	0.901
43DAP/reference	0.94955	0.448
47DAP/reference	1.01806	0.593
52DAP/reference	1.03206	0.607
57DAP/reference	1.14373	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96087	0.496
27DAP/17DAP	0.99007	0.919
39DAP/27DAP	0.94526	0.388
41DAP/39DAP	1.04401	0.727
42DAP/41DAP	0.98964	0.85
43DAP/42DAP	1.03799	0.112
47DAP/43DAP	1.01533	0.889
52DAP/47DAP	1.00065	1
57DAP/52DAP	0.91034	0.322
57DAP/7DAP	0.9908	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92428	0.115
17DAP/reference	0.82137	0.124
27DAP/reference	0.83419	0.071
39DAP/reference	0.88495	0.095
41DAP/reference	0.94675	0.357
42DAP/reference	0.94756	0.355
43DAP/reference	0.99234	0.608
47DAP/reference	0.89997	0.383
52DAP/reference	1.03743	0.832
57DAP/reference	1.00894	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02896	0.634
17DAP/reference	1.05558	0.437
27DAP/reference	0.95183	0.34
39DAP/reference	0.94266	0.257
41DAP/reference	0.98915	0.545
42DAP/reference	1.08548	0.294
43DAP/reference	1.01862	0.735
47DAP/reference	1.127	0.02
52DAP/reference	1.04517	0.368
57DAP/reference	1.06037	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83827	0.092
17DAP/reference	0.95768	0.601
27DAP/reference	0.85992	0.076
39DAP/reference	0.87409	0.111
41DAP/reference	0.85197	0.046
42DAP/reference	0.82608	0.032
43DAP/reference	0.90997	0.076
47DAP/reference	1.04252	0.372
52DAP/reference	0.899	0.385
57DAP/reference	0.94589	0.158

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98799	1
26DAP/20DAP	1.07429	0.785
34DAP/26DAP	0.9744	0.898
51DAP/34DAP	1.04771	0.666
52DAP/51DAP	0.94022	1
53DAP/52DAP	0.98749	0.938
55DAP/53DAP	0.95337	0.709
57DAP/55DAP	0.94415	0.757
62DAP/57DAP	0.99353	1
68DAP/62DAP	1.12445	0.722
68DAP/14DAP	1.28599	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96857	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80356	0.377
Mature Green Tomato/Ripe Tomato	0.82128	0.226
Immature Eggplant/Mature Eggplant	1.09651	0.606
Ripe Pepper/Ripe Tomato	0.98962	1
Mature Eggplant/Ripe Tomato	1.03355	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98707	0.961
1-1-2/M82	0.72273	1
12-2/M82	0.98752	1
12-4/M82	1.00593	1
1-3/M82	1.04589	1
2-1-1/M82	0.93245	0.683
2-1/M82	1.06949	1
2-6/M82	0.9605	1
3-2/M82	0.9812	1
4-1-1/M82	1.06041	1
4-1/M82	0.9022
4-3-2/M82	0.98693	1
4-3/M82	0.96458	0.72
5-3/M82	0.9897	1
6-2/M82	1.01105	1
6-3/M82	1.03704	1
7-1/M82	1.04139	1
7-2/M82	0.94391	0.881
9-3-2/M82	0.91533	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04842
IL2-6/WTpooled	1.17784	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83191	0.418
IL12-4/WTpooled	1.00712	1
IL1-4/WTpooled	1.04126	1
WT/WTpooled	0.88431	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	1.09097	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11152	0.758
DC3000/delta hrp 6h	1.23658	1
DC3000/delta hrp 12h	0.92124	1
DC3000/delta hrp 24h	1.12748	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12191	0.094
DC3000 delta B/DC3000 delta AB	1.05723	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06955	1
Exp 36h	0.79023	0.406
Exp 60h	1.2253	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96621	1
Var 0h	0.98118	1
Var 12h I row2-row1	1.12767	0.209
Var 12h NI row2-row1	0.99652	1
Var 36h I row2-row1	1.00853	1
Var 36h NI row2-row1	0.91061	0.478
Var 60h I row2-row1	1.07698	1
Var 60h NI row2-row1	1.09313	0.904
Time course 0hI-0hNI	1.02434	1
Time course 12hI-12hNI	1.07656	0.493
Time course 36hI-36hNI	1.13909	0.017
Time course 60hI-60hNI	1.27865	0.029

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)	0.92715	0.338
transgenic ySAMdc/azygous control (breaker)	1.48132	0.248
transgenic ySAMdc/azygous control (red)	1.05086	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98384	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75961	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.67885	0.299
Manapal/WT (red)	0.78019	0.229