Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97003	0.77
27DAP/17DAP	0.85728	0.631
39DAP/27DAP	0.77488	0.41
41DAP/39DAP	1.48147	0.265
42DAP/41DAP	1.2296	0.899
43DAP/42DAP	1.03527	1
47DAP/43DAP	1.15201	0.52
52DAP/47DAP	1.25539	0.696
57DAP/52DAP	0.94895	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97328	0.526
17DAP/reference	1.00006	1
27DAP/reference	1.0154	0.863
39DAP/reference	1.01078	0.771
41DAP/reference	1.05124	0.48
42DAP/reference	0.92288	0.04
43DAP/reference	1.03071	0.596
47DAP/reference	0.87809	0.006
52DAP/reference	0.814	0.102
57DAP/reference	0.8117	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01402	0.975
27DAP/17DAP	1.02745	0.942
39DAP/27DAP	1.10538	0.378
41DAP/39DAP	1.03421	1
42DAP/41DAP	1.05031	0.893
43DAP/42DAP	1.01018	0.83
47DAP/43DAP	1.05388	0.765
52DAP/47DAP	1.00557	0.982
57DAP/52DAP	1.00453	1
57DAP/7DAP	1.04635	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56298	0.029
17DAP/reference	1.65494	0.008
27DAP/reference	1.54945	0.008
39DAP/reference	2.15007	0.005
41DAP/reference	2.02318	0.011
42DAP/reference	2.30016	0.007
43DAP/reference	2.34561	0.006
47DAP/reference	1.31618	0.44
52DAP/reference	1.81295	0.007
57DAP/reference	1.85229	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09423	0.181
17DAP/reference	0.98007	0.548
27DAP/reference	0.981	0.576
39DAP/reference	0.86227	0.214
41DAP/reference	0.82823	0.008
42DAP/reference	1.07214	0.723
43DAP/reference	0.88627	0.292
47DAP/reference	0.88551	0.046
52DAP/reference	0.89675	0.187
57DAP/reference	1.03923	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51729	0.031
17DAP/reference	1.23551	0.206
27DAP/reference	1.60285	0.018
39DAP/reference	1.40253	0.013
41DAP/reference	1.43986	0.145
42DAP/reference	1.48657	0.327
43DAP/reference	1.31265	0.646
47DAP/reference	0.96996	0.494
52DAP/reference	1.38488	0.167
57DAP/reference	0.71787	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02644	0.966
26DAP/20DAP	0.92646	1
34DAP/26DAP	1.06135	1
51DAP/34DAP	0.97631	0.807
52DAP/51DAP	1.01569	0.808
53DAP/52DAP	1.11889	0.643
55DAP/53DAP	1.02775	0.964
57DAP/55DAP	1.07983	0.818
62DAP/57DAP	1.05543
68DAP/62DAP	0.92703	0.429
68DAP/14DAP	0.62145	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1031	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.46914	0.106
Mature Green Tomato/Ripe Tomato	1.282	0.437
Immature Eggplant/Mature Eggplant	0.91533	0.493
Ripe Pepper/Ripe Tomato	6.76099	0.256
Mature Eggplant/Ripe Tomato	2.33415	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91994	0.944
1-1-2/M82	0.77103	0.804
12-2/M82	1.14915	1
12-4/M82	0.87853	1
1-3/M82	0.96425	1
2-1-1/M82	1.01263	1
2-1/M82	1.12466	1
2-6/M82	1.00715	1
3-2/M82	N/A	N/A
4-1-1/M82	1.182	1
4-1/M82	0.88245	1
4-3-2/M82	0.85998	0.698
4-3/M82	0.87107	1
5-3/M82	0.87191	0.642
6-2/M82	0.99322	1
6-3/M82	0.95874	1
7-1/M82	1.0439
7-2/M82	1.02539	1
9-3-2/M82	0.88442	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99275	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.10827	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.14729	1
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	0.84588	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05837	0.914
DC3000/delta hrp 6h	1.13794	1
DC3000/delta hrp 12h	1.05963	1
DC3000/delta hrp 24h	0.96295	0.736

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9597	0.436
DC3000 delta B/DC3000 delta AB	0.99912	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.69615	0.397
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	N/A	N/A
Var 0h	0.95025	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.99559	0.931
transgenic ySAMdc/azygous control (breaker)	0.85643	0.134
transgenic ySAMdc/azygous control (red)	0.99517	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00437	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11049	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14642	0.105
Manapal/WT (break)	1.19746	0.183
Manapal/WT (red)	1.35136	0.222