Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84691	0.364
27DAP/17DAP	0.97346	0.957
39DAP/27DAP	1.02077	0.733
41DAP/39DAP	1.2098	0.691
42DAP/41DAP	1.12118	0.938
43DAP/42DAP	1.26336	0.906
47DAP/43DAP	1.2697	0.332
52DAP/47DAP	0.94452	0.812
57DAP/52DAP	0.71713	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90557	0.085
17DAP/reference	0.96347	0.342
27DAP/reference	0.97609	0.61
39DAP/reference	1.06408	0.129
41DAP/reference	1.02185	0.855
42DAP/reference	0.85429	0.03
43DAP/reference	0.96922	0.594
47DAP/reference	1.01408	0.937
52DAP/reference	0.94229	0.267
57DAP/reference	1.03066	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81677	0.26
27DAP/17DAP	1.10706	0.576
39DAP/27DAP	0.89283	0.456
41DAP/39DAP	0.95405	0.893
42DAP/41DAP	1.13147	0.976
43DAP/42DAP	0.92478	0.466
47DAP/43DAP	1.01086	0.989
52DAP/47DAP	0.92589	0.686
57DAP/52DAP	1.38733	0.67
57DAP/7DAP	0.85777	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92093	0.402
17DAP/reference	1.6164	0.007
27DAP/reference	1.65504	0.006
39DAP/reference	2.20269	0.006
41DAP/reference	2.4322	0.011
42DAP/reference	2.87465	0.006
43DAP/reference	2.52029	0.007
47DAP/reference	1.50126	0.272
52DAP/reference	1.95508	0.007
57DAP/reference	1.83436	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90681	0.277
17DAP/reference	1.0231	0.892
27DAP/reference	1.02119	0.765
39DAP/reference	0.84562	0.093
41DAP/reference	0.8257	0.054
42DAP/reference	1.1113	0.466
43DAP/reference	1.10695	0.809
47DAP/reference	1.05913	0.321
52DAP/reference	0.88708	0.28
57DAP/reference	0.85087	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29312	0.046
17DAP/reference	1.2276	0.243
27DAP/reference	1.87161	0.016
39DAP/reference	1.50681	0.006
41DAP/reference	1.57337	0.009
42DAP/reference	1.40584	0.023
43DAP/reference	1.41997	0.223
47DAP/reference	0.92201	0.296
52DAP/reference	1.63524	0.083
57DAP/reference	0.80051	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96441	1
26DAP/20DAP	0.99219	1
34DAP/26DAP	1.01331	1
51DAP/34DAP	0.94649	0.722
52DAP/51DAP	1.00367	1
53DAP/52DAP	1.39552	0.07
55DAP/53DAP	0.85854	0.489
57DAP/55DAP	1.10198	0.854
62DAP/57DAP	0.91154	0.681
68DAP/62DAP	0.76334	0.166
68DAP/14DAP	0.60399	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92804	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.66814	0.187
Mature Green Tomato/Ripe Tomato	1.10165	1
Immature Eggplant/Mature Eggplant	1.39242	0.058
Ripe Pepper/Ripe Tomato	2.00607	0.258
Mature Eggplant/Ripe Tomato	1.09705	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99744	1
1-1-2/M82	1.05138	1
12-2/M82	1.11878	0.61
12-4/M82	1.264	0.611
1-3/M82	0.79135	0.441
2-1-1/M82	1.19296	0.343
2-1/M82	N/A	N/A
2-6/M82	0.98051	1
3-2/M82	0.99193
4-1-1/M82	0.88318	1
4-1/M82	1.23421	0.853
4-3-2/M82	1.09368	1
4-3/M82	0.96821	1
5-3/M82	0.95263	1
6-2/M82	0.80632
6-3/M82	1.26793
7-1/M82	N/A	N/A
7-2/M82	0.94853	1
9-3-2/M82	1.44488	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10027	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9971	1
IL12-4/WTpooled	0.93769	1
IL1-4/WTpooled	1.16425	1
WT/WTpooled	1.06281	0.87

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	0.97734	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14868	0.914
DC3000/delta hrp 6h	1.01325	0.95
DC3000/delta hrp 12h	0.88909	1
DC3000/delta hrp 24h	0.94473	0.607

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	0.81847	0.103

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1053	1
Exp 36h	0.81348	0.661
Exp 60h	0.81635	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97717	1
Var 0h	0.79688	1
Var 12h I row2-row1	0.87311	0.338
Var 12h NI row2-row1	0.94639	0.488
Var 36h I row2-row1	1.1811	0.489
Var 36h NI row2-row1	1.26282	0.482
Var 60h I row2-row1	0.93935	0.285
Var 60h NI row2-row1	1.0205	1
Time course 0hI-0hNI	0.94389	0.516
Time course 12hI-12hNI	0.88034	0.228
Time course 36hI-36hNI	0.84367	0.043
Time course 60hI-60hNI	0.35164	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)	0.91916	0.315
transgenic ySAMdc/azygous control (breaker)	0.84437	0.173
transgenic ySAMdc/azygous control (red)	1.05108	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00673	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59392	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.53938	0.093
Manapal/WT (break)	1.24583	0.183
Manapal/WT (red)	1.30556	0.142