Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10006	0.681
27DAP/17DAP	0.85685	0.626
39DAP/27DAP	0.88184	0.507
41DAP/39DAP	1.07304	0.642
42DAP/41DAP	0.97951	1
43DAP/42DAP	0.79351	0.643
47DAP/43DAP	0.77469	0.321
52DAP/47DAP	0.87938	0.668
57DAP/52DAP	1.10918	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98035	0.55
17DAP/reference	0.8932	0.097
27DAP/reference	1.00407	0.923
39DAP/reference	0.92183	0.164
41DAP/reference	0.89727	0.085
42DAP/reference	1.01973	1
43DAP/reference	1.10502	0.083
47DAP/reference	1.06126	0.223
52DAP/reference	1.00345	1
57DAP/reference	1.175	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95429	0.595
27DAP/17DAP	0.85988	0.227
39DAP/27DAP	1.07056	0.575
41DAP/39DAP	1.20854	0.603
42DAP/41DAP	1.11964	0.087
43DAP/42DAP	1.11499	0.297
47DAP/43DAP	0.93294	0.476
52DAP/47DAP	0.79065	0.372
57DAP/52DAP	0.89892	0.448
57DAP/7DAP	1.11512

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99561	0.682
17DAP/reference	1.12789	0.399
27DAP/reference	1.29227	0.017
39DAP/reference	1.24232	0.066
41DAP/reference	1.17426	0.251
42DAP/reference	1.28835	0.059
43DAP/reference	1.40562	0.008
47DAP/reference	1.19545	0.127
52DAP/reference	1.02109	0.832
57DAP/reference	1.07332	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95176	0.58
17DAP/reference	0.84627	0.013
27DAP/reference	1.01094	0.765
39DAP/reference	0.92603	0.235
41DAP/reference	1.04059	0.629
42DAP/reference	0.90427	0.169
43DAP/reference	0.93738	0.414
47DAP/reference	1.02684	0.943
52DAP/reference	0.95497	0.203
57DAP/reference	0.77481	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02792	1
17DAP/reference	1.09109	0.578
27DAP/reference	1.18012	0.088
39DAP/reference	1.29341	0.022
41DAP/reference	1.20003	0.016
42DAP/reference	1.35176	0.036
43DAP/reference	1.09347	0.667
47DAP/reference	0.78531	0.114
52DAP/reference	1.00002	0.888
57DAP/reference	1.00548	0.858

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94626	1
26DAP/20DAP	1.00801	1
34DAP/26DAP	1.00914	1
51DAP/34DAP	0.924	0.667
52DAP/51DAP	0.80486	1
53DAP/52DAP	1.26705	0.413
55DAP/53DAP	0.78724	0.21
57DAP/55DAP	1.50431	0.106
62DAP/57DAP	0.2535
68DAP/62DAP	0.94716	0.885
68DAP/14DAP	0.94128

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44135	0.049

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.28917	0.068
Mature Green Tomato/Ripe Tomato	0.80993	0.06
Immature Eggplant/Mature Eggplant	1.58344	0.05
Ripe Pepper/Ripe Tomato	0.94123	1
Mature Eggplant/Ripe Tomato	1.60043	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19543	0.551
1-1-2/M82	0.70608
12-2/M82	1.22292
12-4/M82	0.95337	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	0.96177	1
3-2/M82	1.12769
4-1-1/M82	N/A	N/A
4-1/M82	1.65079
4-3-2/M82	N/A	N/A
4-3/M82	1.36947	1
5-3/M82	0.97388	0.642
6-2/M82	N/A	N/A
6-3/M82	0.91477
7-1/M82	1.0371	1
7-2/M82	0.84315	0.881
9-3-2/M82	1.26854

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.68077	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.77635	1
IL12-4/WTpooled	0.95253	1
IL1-4/WTpooled	0.95619
WT/WTpooled	1.05195	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	0.99198	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08169	0.758
DC3000/delta hrp 6h	0.91641	0.95
DC3000/delta hrp 12h	1.04119	1
DC3000/delta hrp 24h	0.97805	0.897

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93766	1
Exp 36h	1.20752	0.693
Exp 60h	1.30741	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00933	1
Var 0h	0.83217	0.933
Var 12h I row2-row1	1.18287	0.58
Var 12h NI row2-row1	0.98395	1
Var 36h I row2-row1	0.98563	1
Var 36h NI row2-row1	1.56787	1
Var 60h I row2-row1	0.87173	0.439
Var 60h NI row2-row1	0.94906	0.516
Time course 0hI-0hNI	1.02043	0.852
Time course 12hI-12hNI	1.09708	0.115
Time course 36hI-36hNI	1.13849	0.011
Time course 60hI-60hNI	2.03807	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)	1.04831	0.571
transgenic ySAMdc/azygous control (breaker)	0.77114	0.142
transgenic ySAMdc/azygous control (red)	0.95418	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0167	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86881	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92627	1
Manapal/WT (break)	0.98206	1
Manapal/WT (red)	0.67017	0.181