Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.15.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.85298	0.101
27DAP/17DAP	1.09832	0.871
39DAP/27DAP	1.40711	0.449
41DAP/39DAP	1.20946	0.67
42DAP/41DAP	1.12035	1
43DAP/42DAP	1.06906	0.937
47DAP/43DAP	2.49199	0.208
52DAP/47DAP	0.8847	0.564
57DAP/52DAP	1.43168	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78873	0.028
17DAP/reference	1.11731	0.143
27DAP/reference	1.16246	0.2
39DAP/reference	1.12363	0.153
41DAP/reference	1.16504	0.027
42DAP/reference	0.93106	0.033
43DAP/reference	1.149	0.152
47DAP/reference	1.32818	0.022
52DAP/reference	1.73842	0.009
57DAP/reference	1.19476	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.8609	0.068
27DAP/17DAP	1.22294	0.253
39DAP/27DAP	1.55027	0.056
41DAP/39DAP	0.69378	0.047
42DAP/41DAP	1.26524	0.155
43DAP/42DAP	0.87184	0.082
47DAP/43DAP	0.95759	0.796
52DAP/47DAP	1.6683	0.074
57DAP/52DAP	0.78539	0.128
57DAP/7DAP	1.95049	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72778	0.062
17DAP/reference	0.83072	0.108
27DAP/reference	0.86693	0.117
39DAP/reference	1.36932	0.022
41DAP/reference	0.93202	0.311
42DAP/reference	1.30783	0.076
43DAP/reference	1.09443	0.432
47DAP/reference	1.62973	0.045
52DAP/reference	0.89021	0.137
57DAP/reference	0.79779	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92013	0.353
17DAP/reference	0.76689	0.011
27DAP/reference	0.83274	0.039
39DAP/reference	0.983	0.539
41DAP/reference	0.83321	0.049
42DAP/reference	0.91352	0.081
43DAP/reference	0.81884	0.019
47DAP/reference	0.88853	0.044
52DAP/reference	0.86465	0.037
57DAP/reference	0.8802	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67233	0.026
17DAP/reference	0.81507	0.239
27DAP/reference	0.73891	0.031
39DAP/reference	0.86815	0.069
41DAP/reference	0.82402	0.032
42DAP/reference	0.95818	0.445
43DAP/reference	0.87402	0.064
47DAP/reference	0.99246	0.61
52DAP/reference	1.31867	0.098
57DAP/reference	0.938	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07812	0.966
26DAP/20DAP	0.71784	0.512
34DAP/26DAP	1.02162
51DAP/34DAP	1.43428	0.352
52DAP/51DAP	1.11535	0.904
53DAP/52DAP	1.18012	0.444
55DAP/53DAP	1.00392	0.852
57DAP/55DAP	0.81148	0.297
62DAP/57DAP	0.9149	0.681
68DAP/62DAP	1.124	1
68DAP/14DAP	0.5705	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.2905	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70686
Mature Green Tomato/Ripe Tomato	0.52102	0.017
Immature Eggplant/Mature Eggplant	2.58922
Ripe Pepper/Ripe Tomato	0.13865	0.224
Mature Eggplant/Ripe Tomato	0.17265	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.27269	0.877
1-1-2/M82	1.11837	1
12-2/M82	0.71501	0.862
12-4/M82	1.10302	1
1-3/M82	1.29132	0.479
2-1-1/M82	1.45829	0.689
2-1/M82	0.93186	0.74
2-6/M82	0.921	1
3-2/M82	1.19557	0.549
4-1-1/M82	1.4242	0.977
4-1/M82	N/A	N/A
4-3-2/M82	1.5446	1
4-3/M82	1.33821	1
5-3/M82	1.11295	1
6-2/M82	1.25948
6-3/M82	1.04503	1
7-1/M82	1.51925	0.992
7-2/M82	1.05591	1
9-3-2/M82	0.89482

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	0.84799
IL7-3/WTpooled	3.5004	1
IL12-4/WTpooled	1.57927	0.546
IL1-4/WTpooled	1.19315	1
WT/WTpooled	1.04116	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	1.25912

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96409	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.15384	1
DC3000/delta hrp 24h	0.72643	0.036

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97105	1
Exp 36h	0.74388	0.504
Exp 60h	0.90078	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99208	1
Var 0h	1.199	0.421
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.93511	0.906
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	1.38783
Var 60h I row2-row1	1.34373	0.543
Var 60h NI row2-row1	0.75007	0.866
Time course 0hI-0hNI	1.13605	0.486
Time course 12hI-12hNI	1.67511	0.593
Time course 36hI-36hNI	1.46317	0.28
Time course 60hI-60hNI	2.62801	0.008

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)	1.0823	0.482
transgenic ySAMdc/azygous control (breaker)	2.15778	0.178
transgenic ySAMdc/azygous control (red)	0.714	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04016	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04548	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.59237	0.172
Manapal/WT (break)	0.94059	1
Manapal/WT (red)	1.10027	0.413