Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00231	0.938
27DAP/17DAP	1.18853	0.833
39DAP/27DAP	1.40522	0.579
41DAP/39DAP	1.21627	0.619
42DAP/41DAP	0.981	1
43DAP/42DAP	1.53188	0.848
47DAP/43DAP	0.94489	0.799
52DAP/47DAP	0.85124	0.605
57DAP/52DAP	0.99516	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46108	0.008
17DAP/reference	1.28168	0.037
27DAP/reference	1.11877	0.33
39DAP/reference	1.21628	0.035
41DAP/reference	1.28466	0.041
42DAP/reference	1.27438	0.001
43DAP/reference	1.1704	0.118
47DAP/reference	1.23222	0.009
52DAP/reference	1.17077	0.03
57DAP/reference	0.93398	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94789	0.595
27DAP/17DAP	0.87531	0.418
39DAP/27DAP	0.95409	0.795
41DAP/39DAP	1.07358	1
42DAP/41DAP	1.08683	0.8
43DAP/42DAP	0.89311	0.336
47DAP/43DAP	1.05835	0.914
52DAP/47DAP	0.87508	0.56
57DAP/52DAP	0.92788	0.587
57DAP/7DAP	0.96336	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10765	0.231
17DAP/reference	0.84611	0.108
27DAP/reference	0.9521	0.348
39DAP/reference	0.80756	0.021
41DAP/reference	0.84564	0.064
42DAP/reference	0.80279	0.019
43DAP/reference	0.83115	0.047
47DAP/reference	0.98049	0.671
52DAP/reference	0.83327	0.04
57DAP/reference	0.8097	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21563	0.085
17DAP/reference	1.49264	0.018
27DAP/reference	1.39662	0.16
39DAP/reference	1.12271	0.514
41DAP/reference	1.42114	0.035
42DAP/reference	1.24624	0.013
43DAP/reference	1.32852	0.038
47DAP/reference	1.27873	0.022
52DAP/reference	1.04806	0.988
57DAP/reference	1.37198	0.083

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92711	0.268
17DAP/reference	1.0367	0.932
27DAP/reference	0.89912	0.165
39DAP/reference	0.85454	0.046
41DAP/reference	1.00757	1
42DAP/reference	0.90654	0.445
43DAP/reference	0.94145	0.432
47DAP/reference	0.92885	0.269
52DAP/reference	0.75744	0.141
57DAP/reference	0.97244	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.48523	0.752
26DAP/20DAP	0.8156	0.317
34DAP/26DAP	1.07664	1
51DAP/34DAP	0.91569	0.508
52DAP/51DAP	1.11661	0.377
53DAP/52DAP	1.18127	0.678
55DAP/53DAP	1.28072	0.555
57DAP/55DAP	1.31379	0.818
62DAP/57DAP	1.23151	0.868
68DAP/62DAP	0.87957	0.668
68DAP/14DAP	0.70206	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05323	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.92121	0.417
Mature Green Tomato/Ripe Tomato	1.19082	0.166
Immature Eggplant/Mature Eggplant	0.99182
Ripe Pepper/Ripe Tomato	1.11119	1
Mature Eggplant/Ripe Tomato	1.46526

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96272	0.907
1-1-2/M82	0.91303	1
12-2/M82	1.07967	1
12-4/M82	1.13388	1
1-3/M82	0.88573	0.501
2-1-1/M82	1.11013	0.689
2-1/M82	1.18795	1
2-6/M82	1.00034	1
3-2/M82	0.88164
4-1-1/M82	0.84559	0.962
4-1/M82	N/A	N/A
4-3-2/M82	0.74232
4-3/M82	0.8549	1
5-3/M82	0.9267	1
6-2/M82	1.06965	1
6-3/M82	1.07732	1
7-1/M82	0.89786	0.509
7-2/M82	1.08764	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75522	0.247
IL2-6/WTpooled	1.00445	1
IL7-5/WTpooled	0.9114	1
IL7-3/WTpooled	0.69256	0.298
IL12-4/WTpooled	0.96796	1
IL1-4/WTpooled	0.79595	0.699
WT/WTpooled	1.09797	0.874

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	0.58288	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91012	0.868
DC3000/delta hrp 6h	1.15093	1
DC3000/delta hrp 12h	1.22527	1
DC3000/delta hrp 24h	1.13558	0.095

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	0.82179	0.47

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24116	1
Exp 36h	1.17865	1
Exp 60h	1.05046	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96696	1
Var 0h	0.9356	1
Var 12h I row2-row1	1.00752	1
Var 12h NI row2-row1	0.89959	0.546
Var 36h I row2-row1	1.13879	1
Var 36h NI row2-row1	2.12325	1
Var 60h I row2-row1	0.9917	1
Var 60h NI row2-row1	1.07465	0.904
Time course 0hI-0hNI	0.93398	0.373
Time course 12hI-12hNI	0.95107	0.782
Time course 36hI-36hNI	0.76017	0.023
Time course 60hI-60hNI	0.32897	0.005

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)	0.99197	0.931
transgenic ySAMdc/azygous control (breaker)	1.13637	1
transgenic ySAMdc/azygous control (red)	0.97324	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00747	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95339	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.54588	0.105
Manapal/WT (break)	1.39659	0.183
Manapal/WT (red)	0.9769	0.863