Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.10876	0.014
27DAP/17DAP	0.68405	0.182
39DAP/27DAP	0.71249	0.241
41DAP/39DAP	1.01155	0.772
42DAP/41DAP	1.54738	0.1
43DAP/42DAP	1.06809	1
47DAP/43DAP	0.81996	0.444
52DAP/47DAP	1.56707	0.23
57DAP/52DAP	1.30781	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14857	0.047
17DAP/reference	0.58777	0.009
27DAP/reference	0.70641	0.037
39DAP/reference	0.61078	0.015
41DAP/reference	0.80151	0.267
42DAP/reference	0.79055	0.026
43DAP/reference	0.65482
47DAP/reference	0.85189	0.071
52DAP/reference	0.85664	0.06
57DAP/reference	0.53602

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.11523	0.016
27DAP/17DAP	0.82678	0.39
39DAP/27DAP	0.77666	0.038
41DAP/39DAP	1.15346	0.727
42DAP/41DAP	0.73213	0.076
43DAP/42DAP	1.02142	0.875
47DAP/43DAP	1.28863	0.448
52DAP/47DAP	1.04731	0.939
57DAP/52DAP	1.04838	1
57DAP/7DAP	0.14877	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8351	0.034
17DAP/reference	1.52681	0.006
27DAP/reference	1.36491	0.03
39DAP/reference	1.35537	0.021
41DAP/reference	1.40796	0.027
42DAP/reference	1.28013	0.076
43DAP/reference	1.59324	0.008
47DAP/reference	1.12771	0.717
52DAP/reference	1.48535	0.013
57DAP/reference	1.52358	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64224	0.1
17DAP/reference	0.49586	0.003
27DAP/reference	0.6495	0.014
39DAP/reference	0.64702	0.01
41DAP/reference	0.73016	0.023
42DAP/reference	0.80242	0.055
43DAP/reference	0.55557	0.004
47DAP/reference	0.74371	0.012
52DAP/reference	0.74238	0.01
57DAP/reference	0.52496	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.07425	0.052
17DAP/reference	1.03527	0.763
27DAP/reference	1.65689	0.023
39DAP/reference	1.44032	0.046
41DAP/reference	1.36739	0.017
42DAP/reference	1.2657	0.175
43DAP/reference	1.34522	0.439
47DAP/reference	0.72553	0.012
52DAP/reference	1.19787	0.517
57DAP/reference	1.17976	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18892	0.966
26DAP/20DAP	2.11199	0.105
34DAP/26DAP	0.43078	0.05
51DAP/34DAP	0.32712	0.049
52DAP/51DAP	0.94491	1
53DAP/52DAP	0.76091	0.21
55DAP/53DAP	0.64792	0.053
57DAP/55DAP	1.00935	1
62DAP/57DAP	0.77669	0.466
68DAP/62DAP	2.61748	0.036
68DAP/14DAP	1.06555	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.31564	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.1926	0.058
Mature Green Tomato/Ripe Tomato	0.56986
Immature Eggplant/Mature Eggplant	0.71335	0.077
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	33.1032	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16087	0.877
1-1-2/M82	0.93396	1
12-2/M82	0.92503
12-4/M82	1.11471	1
1-3/M82	0.76326	0.441
2-1-1/M82	0.84662	0.465
2-1/M82	N/A	N/A
2-6/M82	0.84155	1
3-2/M82	0.87434
4-1-1/M82	0.97088	1
4-1/M82	1.46446
4-3-2/M82	N/A	N/A
4-3/M82	0.90065	1
5-3/M82	0.8307	0.642
6-2/M82	0.71857	1
6-3/M82	1.00951	1
7-1/M82	0.92689
7-2/M82	0.85024	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98223	1
IL2-6/WTpooled	1.01148	1
IL7-5/WTpooled	0.85365	1
IL7-3/WTpooled	1.16013	1
IL12-4/WTpooled	1.09102	0.737
IL1-4/WTpooled	1.07477	1
WT/WTpooled	1.09952	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	1.12383

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1056	0.921
DC3000/delta hrp 6h	1.05335	0.95
DC3000/delta hrp 12h	1.01578	1
DC3000/delta hrp 24h	1.01488	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30862	0.073
DC3000 delta B/DC3000 delta AB	1.25323	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85727	1
Exp 36h	3.40353	1
Exp 60h	2.88252	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0295	1
Var 0h	0.99698	1
Var 12h I row2-row1	2.49583	0.58
Var 12h NI row2-row1	1.1671	1
Var 36h I row2-row1	0.76424	0.805
Var 36h NI row2-row1	3.21934	1
Var 60h I row2-row1	1.11312	1
Var 60h NI row2-row1	1.31831	0.904
Time course 0hI-0hNI	0.80001	0.061
Time course 12hI-12hNI	1.0491	0.741
Time course 36hI-36hNI	0.98972	0.411
Time course 60hI-60hNI	1.99636	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)	1.01081	1
transgenic ySAMdc/azygous control (breaker)	0.82873	0.173
transgenic ySAMdc/azygous control (red)	0.9462	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98647	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59472	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.56181	1
Manapal/WT (break)	0.99119	1
Manapal/WT (red)	0.89875	0.607