Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11641	0.827
27DAP/17DAP	0.46554	0.027
39DAP/27DAP	0.59713	0.304
41DAP/39DAP	0.64041	0.059
42DAP/41DAP	0.84962	0.774
43DAP/42DAP	1.23602	0.869
47DAP/43DAP	0.7065	0.185
52DAP/47DAP	0.87232	0.639
57DAP/52DAP	1.15816	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59994	0.015
17DAP/reference	1.13081	0.148
27DAP/reference	1.05077	0.794
39DAP/reference	1.18374	0.027
41DAP/reference	1.17442	0.026
42DAP/reference	1.32506	0.002
43DAP/reference	1.31743	0.011
47DAP/reference	1.16951	0.264
52DAP/reference	1.03761	1
57DAP/reference	1.05326	0.564

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.63901	0.036
27DAP/17DAP	0.88275	0.724
39DAP/27DAP	0.38585	0.031
41DAP/39DAP	1.29691	0.304
42DAP/41DAP	0.96657	0.746
43DAP/42DAP	0.51456	0.022
47DAP/43DAP	0.78777	0.172
52DAP/47DAP	0.84048	0.098
57DAP/52DAP	0.99492	0.841
57DAP/7DAP	0.23011	0.143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38016	0.038
17DAP/reference	1.12722	0.297
27DAP/reference	1.50589	0.007
39DAP/reference	1.26212	0.046
41DAP/reference	1.36676	0.029
42DAP/reference	1.41268	0.007
43DAP/reference	1.4567	0.008
47DAP/reference	1.14262	0.377
52DAP/reference	1.37286	0.043
57DAP/reference	1.26915	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46565	0.463
17DAP/reference	1.7391	0.007
27DAP/reference	1.36139	0.095
39DAP/reference	1.39534	0.031
41DAP/reference	1.45002	0.007
42DAP/reference	1.45038	0.011
43DAP/reference	1.35616	0.205
47DAP/reference	1.3457	0.008
52DAP/reference	1.20096	0.057
57DAP/reference	1.22394	0.423

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53213	0.015
17DAP/reference	1.12356	0.503
27DAP/reference	1.25437	0.048
39DAP/reference	1.17749	0.038
41DAP/reference	1.23582	0.058
42DAP/reference	1.18698	0.057
43DAP/reference	1.43259	0.033
47DAP/reference	1.09458	0.443
52DAP/reference	1.26872	0.155
57DAP/reference	1.11141	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.63345	0.807
26DAP/20DAP	1.00577	1
34DAP/26DAP	0.83527	0.301
51DAP/34DAP	0.89834	0.571
52DAP/51DAP	1.01018	0.954
53DAP/52DAP	0.81868	0.311
55DAP/53DAP	1.22181	0.547
57DAP/55DAP	1.04625	0.997
62DAP/57DAP	0.858	0.681
68DAP/62DAP	0.94768	0.787
68DAP/14DAP	0.80917	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.69216	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.17526	0.089
Mature Green Tomato/Ripe Tomato	11.1603	0.016
Immature Eggplant/Mature Eggplant	0.90794	0.72
Ripe Pepper/Ripe Tomato	1.27005	1
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.22864	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.2835	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.81196	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97008	1
IL12-4/WTpooled	0.90466	0.71
IL1-4/WTpooled	0.88194	0.415
WT/WTpooled	0.92027	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	0.95879	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.08081	1
DC3000/delta hrp 12h	1.09481	1
DC3000/delta hrp 24h	1.42231	0.099

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65199	0.026
DC3000 delta B/DC3000 delta AB	0.47855	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17327	1
Exp 36h	1.28911	0.693
Exp 60h	1.35185	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00024	1
Var 0h	1.10117	0.782
Var 12h I row2-row1	0.94479	0.338
Var 12h NI row2-row1	0.94058	0.36
Var 36h I row2-row1	1.06215	1
Var 36h NI row2-row1	0.9723	0.706
Var 60h I row2-row1	1.11739	0.562
Var 60h NI row2-row1	1.02053	1
Time course 0hI-0hNI	0.99906	1
Time course 12hI-12hNI	0.99064	0.931
Time course 36hI-36hNI	1.01047	0.975
Time course 60hI-60hNI	0.68393	0.026

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)	0.90648	0.246
transgenic ySAMdc/azygous control (breaker)	0.80606	0.251
transgenic ySAMdc/azygous control (red)	1.04658	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0438	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77575	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87329	0.172
Manapal/WT (break)	1.25272	0.381
Manapal/WT (red)	1.134	0.142