Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98573	0.858
27DAP/17DAP	1.17173	0.809
39DAP/27DAP	0.74336	0.293
41DAP/39DAP	1.34496	0.282
42DAP/41DAP	0.99379	1
43DAP/42DAP	0.98608	0.932
47DAP/43DAP	0.95716	0.815
52DAP/47DAP	1.08038	0.819
57DAP/52DAP	1.06982	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10755	0.218
17DAP/reference	1.06314	0.248
27DAP/reference	1.03257	0.934
39DAP/reference	1.05794	0.474
41DAP/reference	0.93305	0.434
42DAP/reference	1.06729	0.842
43DAP/reference	1.16174	0.083
47DAP/reference	0.99282	0.602
52DAP/reference	0.90228	0.099
57DAP/reference	1.05689	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98197	0.763
27DAP/17DAP	1.00273	1
39DAP/27DAP	1.0517	0.611
41DAP/39DAP	1.06068	0.623
42DAP/41DAP	0.96277	0.644
43DAP/42DAP	1.02008	0.627
47DAP/43DAP	0.96348	0.606
52DAP/47DAP	1.02355	0.907
57DAP/52DAP	1.01187	1
57DAP/7DAP	1.06029	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83563	0.091
17DAP/reference	0.91095	0.011
27DAP/reference	0.89158	0.016
39DAP/reference	0.97562	0.146
41DAP/reference	1.01266	0.918
42DAP/reference	0.98235	0.506
43DAP/reference	0.96896	0.334
47DAP/reference	1.03836	0.776
52DAP/reference	0.95965	0.232
57DAP/reference	0.92442	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09047	0.687
17DAP/reference	0.95396	0.422
27DAP/reference	1.04989	0.757
39DAP/reference	0.95404	0.359
41DAP/reference	0.87609	0.133
42DAP/reference	0.90213	0.212
43DAP/reference	0.99937	0.787
47DAP/reference	0.98469	0.574
52DAP/reference	0.91491	0.121
57DAP/reference	0.88479	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91839	0.061
17DAP/reference	0.9198	0.177
27DAP/reference	0.96286	0.14
39DAP/reference	0.94442	0.111
41DAP/reference	0.95996	0.237
42DAP/reference	0.99396	0.816
43DAP/reference	0.97396	0.384
47DAP/reference	0.8658	0.027
52DAP/reference	0.92316	0.334
57DAP/reference	1.03777	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98295	1
26DAP/20DAP	0.9354	0.512
34DAP/26DAP	0.91484	0.364
51DAP/34DAP	1.0783	0.416
52DAP/51DAP	1.01375	0.821
53DAP/52DAP	0.92705	0.595
55DAP/53DAP	1.01142	0.991
57DAP/55DAP	1.07485	0.51
62DAP/57DAP	0.3954	0.01
68DAP/62DAP	1.13964	0.878
68DAP/14DAP	1.16228	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93901	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98715	0.783
Mature Green Tomato/Ripe Tomato	0.96126	0.774
Immature Eggplant/Mature Eggplant	1.32026	0.053
Ripe Pepper/Ripe Tomato	2.26419	0.256
Mature Eggplant/Ripe Tomato	0.95331	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00563	1
1-1-2/M82	1.0391
12-2/M82	1.07271	1
12-4/M82	0.99689	1
1-3/M82	1.0434	1
2-1-1/M82	1.0357	0.764
2-1/M82	1.18021	1
2-6/M82	1.09066	0.364
3-2/M82	1.01251
4-1-1/M82	0.90596	1
4-1/M82	0.994	1
4-3-2/M82	0.91069	1
4-3/M82	0.9664	1
5-3/M82	1.07718	0.572
6-2/M82	0.97809
6-3/M82	0.96382	0.916
7-1/M82	0.93833	0.803
7-2/M82	0.95267	0.881
9-3-2/M82	0.83231

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	1.32824	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97312	1
DC3000/delta hrp 6h	0.97834	0.95
DC3000/delta hrp 12h	0.88633	1
DC3000/delta hrp 24h	0.98843	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04775	0.229
DC3000 delta B/DC3000 delta AB	1.00222	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7925	0.235
Exp 36h	0.88864	0.699
Exp 60h	0.80268	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97412	1
Var 0h	1.20274	0.782
Var 12h I row2-row1	1.1088	0.283
Var 12h NI row2-row1	1.05909	0.649
Var 36h I row2-row1	0.99518	1
Var 36h NI row2-row1	0.86939	0.421
Var 60h I row2-row1	0.969	0.285
Var 60h NI row2-row1	0.93473	0.818
Time course 0hI-0hNI	1.04309	0.852
Time course 12hI-12hNI	1.02122	0.82
Time course 36hI-36hNI	1.10649	0.28
Time course 60hI-60hNI	1.51111	0.01

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)	1.08195	0.372
transgenic ySAMdc/azygous control (breaker)	0.95231	0.49
transgenic ySAMdc/azygous control (red)	1.00347	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96002	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44092	0.14
Manapal/WT (break)	1.60616	0.14
Manapal/WT (red)	1.39182	0.164