Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10821	0.977
27DAP/17DAP	0.84363	0.661
39DAP/27DAP	0.91013	0.594
41DAP/39DAP	0.99134	0.911
42DAP/41DAP	0.96183	1
43DAP/42DAP	1.05525	1
47DAP/43DAP	1.08119	0.95
52DAP/47DAP	1.04182	1
57DAP/52DAP	1.02163	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18413	0.101
17DAP/reference	1.38131	0.022
27DAP/reference	1.27353	0.048
39DAP/reference	1.16734	0.104
41DAP/reference	1.41789	0.013
42DAP/reference	1.28108	0.002
43DAP/reference	1.13843	0.596
47DAP/reference	1.17634	0.03
52DAP/reference	0.96698	0.461
57DAP/reference	0.77081	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09741	0.65
27DAP/17DAP	1.23925	0.339
39DAP/27DAP	0.91338	0.287
41DAP/39DAP	0.99148	1
42DAP/41DAP	1.10723	0.582
43DAP/42DAP	0.8994	0.256
47DAP/43DAP	0.87331	0.179
52DAP/47DAP	1.12416	0.598
57DAP/52DAP	1.17604	0.286
57DAP/7DAP	0.94595	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81563	0.095
17DAP/reference	1.03439	1
27DAP/reference	1.16283	0.197
39DAP/reference	0.73456	0.056
41DAP/reference	0.95721	0.412
42DAP/reference	1.06609	1
43DAP/reference	0.96729	0.48
47DAP/reference	0.93706	0.504
52DAP/reference	0.96116	0.435
57DAP/reference	1.04138	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24762	0.175
17DAP/reference	1.43805	0.008
27DAP/reference	1.31057	0.089
39DAP/reference	0.90183	0.159
41DAP/reference	0.97816	0.481
42DAP/reference	1.14718	0.359
43DAP/reference	1.1344	0.662
47DAP/reference	1.08942	0.19
52DAP/reference	1.10346	0.417
57DAP/reference	1.08987	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12328	0.676
17DAP/reference	1.15131	0.627
27DAP/reference	1.25349	0.092
39DAP/reference	0.96659	0.464
41DAP/reference	0.99816	0.754
42DAP/reference	1.28763	0.15
43DAP/reference	1.12745	0.59
47DAP/reference	1.92064	0.006
52DAP/reference	0.90141	0.482
57DAP/reference	1.39709	0.066

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94274	1
26DAP/20DAP	0.94739	1
34DAP/26DAP	1.32664	0.819
51DAP/34DAP	1.56913	0.511
52DAP/51DAP	1.57315	0.035
53DAP/52DAP	1.31911	0.051
55DAP/53DAP	1.4468	0.043
57DAP/55DAP	0.92012	0.629
62DAP/57DAP	0.99935	1
68DAP/62DAP	1.18855	0.939
68DAP/14DAP	0.63654	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73712	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.57461	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.44447	0.057
Ripe Pepper/Ripe Tomato	3.3587	0.256
Mature Eggplant/Ripe Tomato	2.07689	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	N/A	N/A
12-4/M82	1.26056	1
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	1.05845
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.49873
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.93802	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.08021
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.40138	0.788
IL7-5/WTpooled	3.3946
IL7-3/WTpooled	0.88855	0.31
IL12-4/WTpooled	0.92809	1
IL1-4/WTpooled	1.01742	1
WT/WTpooled	1.06721	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	0.97484	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01629	0.921
DC3000/delta hrp 6h	1.12371	1
DC3000/delta hrp 12h	1.44276	1
DC3000/delta hrp 24h	1.01151	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88697	0.171
DC3000 delta B/DC3000 delta AB	1.01175	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06329	1
Exp 36h	0.8002	0.661
Exp 60h	0.81953	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0714	1
Var 0h	0.55741	0.98
Var 12h I row2-row1	0.97069	0.856
Var 12h NI row2-row1	0.86689	0.546
Var 36h I row2-row1	1.05735	1
Var 36h NI row2-row1	1.31977	1
Var 60h I row2-row1	6.12814
Var 60h NI row2-row1	0.86121	0.932
Time course 0hI-0hNI	1.00663	1
Time course 12hI-12hNI	0.9203	0.3
Time course 36hI-36hNI	0.78662	0.028
Time course 60hI-60hNI	0.49156	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)	0.95241	0.662
transgenic ySAMdc/azygous control (breaker)	1.16253	1
transgenic ySAMdc/azygous control (red)	1.62515	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01581	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.91195	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.54671	0.083
Manapal/WT (break)	3.15472	0.183
Manapal/WT (red)	4.46147	0.133