Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44026	0.211
27DAP/17DAP	0.51791	0.027
39DAP/27DAP	0.59046	0.328
41DAP/39DAP	0.64333	0.072
42DAP/41DAP	0.66075	0.397
43DAP/42DAP	1.16592	1
47DAP/43DAP	0.3996	0.049
52DAP/47DAP	0.93269	0.812
57DAP/52DAP	1.0844	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68428	0.053
17DAP/reference	0.45826	0.008
27DAP/reference	0.48682	0.013
39DAP/reference	0.40229	0.01
41DAP/reference	0.30355	0.008
42DAP/reference	0.43717	0.001
43DAP/reference	0.34708	0.012
47DAP/reference	0.34207	0.001
52DAP/reference	0.46739	0.034
57DAP/reference	0.5803	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84544	0.036
27DAP/17DAP	0.67855	0.241
39DAP/27DAP	0.30233	0.028
41DAP/39DAP	1.31951	0.015
42DAP/41DAP	0.8249	0.034
43DAP/42DAP	0.47977	0.022
47DAP/43DAP	0.89459	0.332
52DAP/47DAP	0.98543	0.901
57DAP/52DAP	1.35948	0.311
57DAP/7DAP	0.23119	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81687	0.122
17DAP/reference	0.5933	0.011
27DAP/reference	0.38876	0.01
39DAP/reference	0.33419	0.011
41DAP/reference	0.28743	0.009
42DAP/reference	0.28147	0.01
43DAP/reference	0.25587	0.01
47DAP/reference	0.25358	0.026
52DAP/reference	0.31664	0.01
57DAP/reference	0.31447	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38504	0.005
17DAP/reference	0.4398	0.004
27DAP/reference	0.6656	0.058
39DAP/reference	0.39147	0.01
41DAP/reference	0.4557	0.005
42DAP/reference	0.39201	0.012
43DAP/reference	0.25308	0.002
47DAP/reference	0.35047	0.007
52DAP/reference	0.29072	0.003
57DAP/reference	0.19569	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.597	0.021
17DAP/reference	1.4005	0.15
27DAP/reference	0.95812	0.49
39DAP/reference	0.78738	0.037
41DAP/reference	0.51785	0.018
42DAP/reference	0.40111	0.015
43DAP/reference	0.42168	0.017
47DAP/reference	0.32633	0.004
52DAP/reference	0.25903	0.047
57DAP/reference	1.14767	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03502	1
26DAP/20DAP	1.3636	0.39
34DAP/26DAP	0.75587	0.286
51DAP/34DAP	0.36595	0.049
52DAP/51DAP	0.9265	1
53DAP/52DAP	0.55753	0.049
55DAP/53DAP	0.69731	0.067
57DAP/55DAP	0.9156	0.638
62DAP/57DAP	1.55776	0.04
68DAP/62DAP	1.08145	0.827
68DAP/14DAP	0.69628	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.30817	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.28393	0.058
Mature Green Tomato/Ripe Tomato	11.9587	0.015
Immature Eggplant/Mature Eggplant	0.3698	0.057
Ripe Pepper/Ripe Tomato	23.4289	0.256
Mature Eggplant/Ripe Tomato	66.183	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.57548	0.692
12-4/M82	0.61221
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89949
3-2/M82	1.0232
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	2.21849	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.59394
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.98157	1
IL1-4/WTpooled	1.08378
WT/WTpooled	1.0075	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	1.01047	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9283	1
DC3000/delta hrp 6h	0.98178	0.95
DC3000/delta hrp 12h	1.36214	1
DC3000/delta hrp 24h	1.02952	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75139
DC3000 delta B/DC3000 delta AB	0.56152	0.061

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02149	1
Exp 36h	0.83918	0.699
Exp 60h	0.80098	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97097	1
Var 0h	1.04877	0.98
Var 12h I row2-row1	0.84654	0.357
Var 12h NI row2-row1	0.93585	0.627
Var 36h I row2-row1	0.859	0.805
Var 36h NI row2-row1	0.99125	1
Var 60h I row2-row1	1.71996	0.562
Var 60h NI row2-row1	1.04211	1
Time course 0hI-0hNI	0.98953	0.999
Time course 12hI-12hNI	0.98724	0.893
Time course 36hI-36hNI	0.91356	0.053
Time course 60hI-60hNI	0.27687	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)	1.08696	0.798
transgenic ySAMdc/azygous control (breaker)	3.35999	0.165
transgenic ySAMdc/azygous control (red)	1.58007	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.42328	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.94667	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	20.6834	0.083
Manapal/WT (break)	8.82659	0.123
Manapal/WT (red)	3.92589	0.413