Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0616	0.851
27DAP/17DAP	0.92831	0.892
39DAP/27DAP	1.28881	0.384
41DAP/39DAP	0.96098	0.825
42DAP/41DAP	1.04553	0.954
43DAP/42DAP	1.20941	1
47DAP/43DAP	0.79762	0.395
52DAP/47DAP	1.22796	0.646
57DAP/52DAP	0.97277	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01107	0.787
17DAP/reference	0.69578	0.01
27DAP/reference	0.93374	0.406
39DAP/reference	0.83814	0.132
41DAP/reference	0.65926	0.014
42DAP/reference	1.16337	0.252
43DAP/reference	0.90905	0.222
47DAP/reference	1.13757	0.264
52DAP/reference	1.30731	0.031
57DAP/reference	1.14471	0.259

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80288	0.105
27DAP/17DAP	1.0629	0.893
39DAP/27DAP	1.00005	0.997
41DAP/39DAP	1.0603	0.455
42DAP/41DAP	1.21955	0.74
43DAP/42DAP	1.15093	0.086
47DAP/43DAP	1.07023	0.822
52DAP/47DAP	0.779	0.085
57DAP/52DAP	1.00467	0.907
57DAP/7DAP	1.22325	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99586	0.682
17DAP/reference	1.19191	0.112
27DAP/reference	0.90918	0.215
39DAP/reference	1.0659	0.411
41DAP/reference	1.16815	0.402
42DAP/reference	0.94957	0.531
43DAP/reference	0.9493	0.292
47DAP/reference	1.052	0.932
52DAP/reference	1.08717	0.375
57DAP/reference	0.99424	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94474	0.564
17DAP/reference	0.93884	0.399
27DAP/reference	1.25004	0.288
39DAP/reference	0.96808	0.509
41DAP/reference	1.3478	0.149
42DAP/reference	1.075	0.621
43DAP/reference	0.88599	0.25
47DAP/reference	0.92276	0.284
52DAP/reference	1.26433	0.038
57DAP/reference	1.0517	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10057	0.311
17DAP/reference	1.15549	0.531
27DAP/reference	0.949	0.442
39DAP/reference	1.05454	0.422
41DAP/reference	1.11731	0.537
42DAP/reference	1.3195	0.082
43DAP/reference	1.42292	0.032
47DAP/reference	0.75971	0.043
52DAP/reference	1.02896	0.99
57DAP/reference	1.77126	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.05493	0.966
26DAP/20DAP	1.06972	1
34DAP/26DAP	1.13818	1
51DAP/34DAP	1.24407	0.524
52DAP/51DAP	0.98925	1
53DAP/52DAP	1.41045	0.108
55DAP/53DAP	1.06415	0.798
57DAP/55DAP	1.18844	0.745
62DAP/57DAP	1.08158	0.935
68DAP/62DAP	1.22358	0.653
68DAP/14DAP	1.5686	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.82144	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.10183	0.058
Mature Green Tomato/Ripe Tomato	0.4524	0.017
Immature Eggplant/Mature Eggplant	0.30856	0.067
Ripe Pepper/Ripe Tomato	0.443
Mature Eggplant/Ripe Tomato	0.83998	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.81503
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	0.70225
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.7068
4-3-2/M82	1.52724
4-3/M82	0.78958	0.611
5-3/M82	0.88613	0.49
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	1.01114	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09812
DC3000/delta hrp 6h	0.93987	0.95
DC3000/delta hrp 12h	1.05066	1
DC3000/delta hrp 24h	0.6564	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65875
DC3000 delta B/DC3000 delta AB	0.76144	0.037

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99548	1
Var 0h	0.97685	1
Var 12h I row2-row1	0.90901	0.357
Var 12h NI row2-row1	1.06441	0.649
Var 36h I row2-row1	1.11915	0.298
Var 36h NI row2-row1	1.10366	1
Var 60h I row2-row1	0.88722	0.832
Var 60h NI row2-row1	0.91086	0.932
Time course 0hI-0hNI	0.95692	0.699
Time course 12hI-12hNI	0.96272	0.618
Time course 36hI-36hNI	1.02512	0.401
Time course 60hI-60hNI	0.94514	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)	0.99064	0.862
transgenic ySAMdc/azygous control (breaker)	0.94604	1
transgenic ySAMdc/azygous control (red)	0.94065	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.3346	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68877	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70366	1
Manapal/WT (break)	1.32178	0.381
Manapal/WT (red)	0.87834	0.424