Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.2.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40335	0.932
27DAP/17DAP	1.07665	0.86
39DAP/27DAP	1.28443	0.285
41DAP/39DAP	0.82731	0.33
42DAP/41DAP	1.25952	0.488
43DAP/42DAP	1.12097	1
47DAP/43DAP	0.9572	0.835
52DAP/47DAP	1.07855	0.906
57DAP/52DAP	1.12107	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8814	0.106
17DAP/reference	0.82501	0.013
27DAP/reference	0.9757	0.668
39DAP/reference	0.90585	0.066
41DAP/reference	0.77746	0.018
42DAP/reference	0.95523	0.134
43DAP/reference	0.92404	0.2
47DAP/reference	1.03503	0.541
52DAP/reference	1.09601	0.951
57DAP/reference	1.2438	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76416	0.135
27DAP/17DAP	1.00107	0.969
39DAP/27DAP	1.30693	0.135
41DAP/39DAP	0.99617	1
42DAP/41DAP	1.02083	0.976
43DAP/42DAP	1.25189	0.066
47DAP/43DAP	0.98247	0.919
52DAP/47DAP	0.84421	0.357
57DAP/52DAP	0.85136	0.422
57DAP/7DAP	0.83907	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22863	0.061
17DAP/reference	1.0943	0.147
27DAP/reference	1.14521	0.131
39DAP/reference	1.45984	0.006
41DAP/reference	1.17684	0.072
42DAP/reference	1.57715	0.009
43DAP/reference	1.44969	0.031
47DAP/reference	1.15996	0.165
52DAP/reference	1.37444	0.007
57DAP/reference	1.40451	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91365	0.238
17DAP/reference	0.85751	0.068
27DAP/reference	1.08136	0.745
39DAP/reference	1.06208	1
41DAP/reference	1.09127	1
42DAP/reference	0.99371	0.655
43DAP/reference	0.9164	0.292
47DAP/reference	0.88485	0.048
52DAP/reference	0.90337	0.093
57DAP/reference	0.82199	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08255	0.709
17DAP/reference	1.00919	0.87
27DAP/reference	1.12398	0.325
39DAP/reference	1.21608	0.189
41DAP/reference	1.2301	0.018
42DAP/reference	1.32345	0.036
43DAP/reference	1.47948	0.025
47DAP/reference	0.9232	0.24
52DAP/reference	1.33689	0.205
57DAP/reference	1.63466	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7215	0.121
26DAP/20DAP	1.35724	N/A
34DAP/26DAP	0.93271	0.509
51DAP/34DAP	0.7003	0.193
52DAP/51DAP	0.60567	0.151
53DAP/52DAP	0.95275	0.797
55DAP/53DAP	1.10511	0.764
57DAP/55DAP	0.8437	0.398
62DAP/57DAP	2.03253	0.902
68DAP/62DAP	1.84169	0.616
68DAP/14DAP	2.38805	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.19535	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89354	0.41
Mature Green Tomato/Ripe Tomato	0.88633	0.522
Immature Eggplant/Mature Eggplant	0.79167	0.105
Ripe Pepper/Ripe Tomato	1.0269	1
Mature Eggplant/Ripe Tomato	0.36464	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1011	0.877
1-1-2/M82	1.19465	1
12-2/M82	0.91614	0.955
12-4/M82	1.1251	1
1-3/M82	1.56988	0.277
2-1-1/M82	1.11998	1
2-1/M82	0.72375	N/A
2-6/M82	1.43335	0.425
3-2/M82	1.25174	0.463
4-1-1/M82	1.43596	0.977
4-1/M82	1.46215	1
4-3-2/M82	1.53043	0.508
4-3/M82	1.43875	0.268
5-3/M82	1.15745	0.572
6-2/M82	N/A	N/A
6-3/M82	1.13006	1
7-1/M82	1.18361	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.48064	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	1.04949	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07069	0.921
DC3000/delta hrp 6h	1.07745	1
DC3000/delta hrp 12h	0.98157	1
DC3000/delta hrp 24h	1.0063	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53661	N/A
DC3000 delta B/DC3000 delta AB	1.15364	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9818	1
Exp 36h	0.93772	0.879
Exp 60h	0.9396	0.855

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	1.6046	0.594
Var 12h I row2-row1	0.80538	0.77
Var 12h NI row2-row1	0.91089	0.82
Var 36h I row2-row1	1.34189	0.283
Var 36h NI row2-row1	1.12256	1
Var 60h I row2-row1	0.57022	N/A
Var 60h NI row2-row1	0.88206	0.572
Time course 0hI-0hNI	0.96815	0.945
Time course 12hI-12hNI	0.95599	0.855
Time course 36hI-36hNI	1.04379	0.881
Time course 60hI-60hNI	1.32832	0.029

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)	1.05273	0.511
transgenic ySAMdc/azygous control (breaker)	1.15068	1
transgenic ySAMdc/azygous control (red)	1.08313	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05901	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77117	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01134	1
Manapal/WT (break)	1.03015	1
Manapal/WT (red)	1.04936	0.125