Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.3.17.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	5.35257	0.017
27DAP/17DAP	0.99509	0.963
39DAP/27DAP	1.68602	0.165
41DAP/39DAP	0.56798	0.045
42DAP/41DAP	0.94785	1
43DAP/42DAP	1.26164	0.873
47DAP/43DAP	0.15696	0.038
52DAP/47DAP	0.87539	0.651
57DAP/52DAP	1.03211	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02707	1
17DAP/reference	1.5965	0.036
27DAP/reference	1.13699	0.161
39DAP/reference	1.38035	0.14
41DAP/reference	1.91295	0.014
42DAP/reference	1.0389	0.645
43DAP/reference	1.2316	0.403
47DAP/reference	0.66482	0.007
52DAP/reference	0.88611	0.162
57DAP/reference	0.80434	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	5.29245	0.036
27DAP/17DAP	0.67031	0.241
39DAP/27DAP	0.8701	0.426
41DAP/39DAP	1.40562	0.98
42DAP/41DAP	0.97202	0.649
43DAP/42DAP	1.74299	0.02
47DAP/43DAP	0.49488	0.008
52DAP/47DAP	2.26347	0.048
57DAP/52DAP	1.34209	0.202
57DAP/7DAP	2.18396	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.35897	0.024
17DAP/reference	1.53126	0.011
27DAP/reference	1.19584	0.02
39DAP/reference	2.12199	0.01
41DAP/reference	1.31594	0.06
42DAP/reference	1.57598	0.037
43DAP/reference	1.34025	0.289
47DAP/reference	1.32978	0.254
52DAP/reference	0.91714	0.106
57DAP/reference	0.88565	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74392	0.079
17DAP/reference	1.28835	0.979
27DAP/reference	0.82796	0.108
39DAP/reference	1.46325	0.041
41DAP/reference	1.0172	0.666
42DAP/reference	1.32189	0.18
43DAP/reference	1.30589	0.188
47DAP/reference	1.19117	0.164
52DAP/reference	1.82719	0.023
57DAP/reference	1.19643	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12686	0.207
17DAP/reference	1.54852	0.091
27DAP/reference	1.24192	0.065
39DAP/reference	1.64184	0.005
41DAP/reference	1.51495	0.008
42DAP/reference	1.03037	0.877
43DAP/reference	1.18262	0.412
47DAP/reference	1.02289	0.667
52DAP/reference	0.93994	0.551
57DAP/reference	1.03006	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.805	0.611
26DAP/20DAP	5.99836	0.04
34DAP/26DAP	1.33587	0.542
51DAP/34DAP	0.8315	0.311
52DAP/51DAP	1.50641	0.048
53DAP/52DAP	0.42461	0.049
55DAP/53DAP	0.53919	0.017
57DAP/55DAP	1.05719	0.986
62DAP/57DAP	0.52548	0.004
68DAP/62DAP	2.85453	0.074
68DAP/14DAP	1.02557	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0591	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	8.83296	0.058
Mature Green Tomato/Ripe Tomato	8.3238	0.015
Immature Eggplant/Mature Eggplant	0.1397	0.057
Ripe Pepper/Ripe Tomato	1.83013	0.258
Mature Eggplant/Ripe Tomato	4.22933	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98998	0.961
1-1-2/M82	1.51993	1
12-2/M82	0.63216	N/A
12-4/M82	1.77484	0.694
1-3/M82	N/A	N/A
2-1-1/M82	0.83864	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	3.55704	0.426
4-1-1/M82	2.11072	N/A
4-1/M82	3.44478	N/A
4-3-2/M82	1.92918	0.508
4-3/M82	1.28734	1
5-3/M82	0.87974	1
6-2/M82	2.28125	N/A
6-3/M82	0.95992	N/A
7-1/M82	N/A	N/A
7-2/M82	2.5609	0.302
9-3-2/M82	1.89186	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99931	1
IL2-6/WTpooled	0.8883	0.473
IL7-5/WTpooled	0.80795	1
IL7-3/WTpooled	1.11462	0.362
IL12-4/WTpooled	0.91888	1
IL1-4/WTpooled	1.00637	1
WT/WTpooled	1.00341	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	0.73982	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13237	0.921
DC3000/delta hrp 6h	0.94166	0.95
DC3000/delta hrp 12h	1.24072	1
DC3000/delta hrp 24h	0.54919	0.034

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	0.41652	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.6761	1
Exp 36h	0.47718	0.406
Exp 60h	0.52617	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03599	1
Var 0h	0.79005	0.933
Var 12h I row2-row1	0.78258	0.353
Var 12h NI row2-row1	1.14806	0.649
Var 36h I row2-row1	0.79777	0.805
Var 36h NI row2-row1	1.08567	1
Var 60h I row2-row1	0.993	N/A
Var 60h NI row2-row1	0.86061	0.756
Time course 0hI-0hNI	0.92534	0.535
Time course 12hI-12hNI	1.00413	1
Time course 36hI-36hNI	0.65021	0.024
Time course 60hI-60hNI	0.30352	0.006

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)	0.96989	0.662
transgenic ySAMdc/azygous control (breaker)	0.50906	0.15
transgenic ySAMdc/azygous control (red)	1.08322	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01089	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.48917	1
Manapal/WT (red)	0.91827	0.36