Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2989	0.272
27DAP/17DAP	1.15392	0.842
39DAP/27DAP	1.23069	0.782
41DAP/39DAP	0.88331	0.53
42DAP/41DAP	0.92458	1
43DAP/42DAP	1.11931	0.954
47DAP/43DAP	1.33038	0.527
52DAP/47DAP	1.60742	0.665
57DAP/52DAP	1.20302	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72812	0.136
17DAP/reference	0.4682	0.012
27DAP/reference	0.86043	0.428
39DAP/reference	0.69261	0.054
41DAP/reference	0.42944	0.018
42DAP/reference	0.7372	0.03
43DAP/reference	0.65116	0.029
47DAP/reference	0.88597	0.191
52DAP/reference	0.74593	0.131
57DAP/reference	1.15566	0.061

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04716	1
27DAP/17DAP	1.26214	0.116
39DAP/27DAP	0.88237
41DAP/39DAP	0.90981	0.599
42DAP/41DAP	0.92401	0.511
43DAP/42DAP	0.87878	0.224
47DAP/43DAP	1.09592	0.901
52DAP/47DAP	1.20978	0.498
57DAP/52DAP	1.09668	0.732
57DAP/7DAP	0.87165	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80697	0.104
17DAP/reference	0.99773	0.599
27DAP/reference	0.99493	0.614
39DAP/reference	1.03164	0.865
41DAP/reference	1.05588	1
42DAP/reference	0.98072	0.531
43DAP/reference	1.03859	1
47DAP/reference	0.67441	0.079
52DAP/reference	0.79474	0.053
57DAP/reference	0.89497	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51285	0.005
17DAP/reference	0.48963	0.003
27DAP/reference	0.73898	0.033
39DAP/reference	0.83154	0.165
41DAP/reference	0.90761	0.25
42DAP/reference	0.79836	0.032
43DAP/reference	0.43596	0.003
47DAP/reference	0.62492	0.012
52DAP/reference	0.68943	0.005
57DAP/reference	0.48287	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94321	0.362
17DAP/reference	0.84912	0.182
27DAP/reference	0.98009	0.594
39DAP/reference	0.83741	0.122
41DAP/reference	0.8595	0.148
42DAP/reference	1.05344	1
43DAP/reference	1.06199	0.894
47DAP/reference	0.59228	0.009
52DAP/reference	1.18209	0.952
57DAP/reference	1.59912	0.106

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97306	1
26DAP/20DAP	1.12179	0.798
34DAP/26DAP	1.09451	1
51DAP/34DAP	1.17297	0.925
52DAP/51DAP	1.3353	0.313
53DAP/52DAP	1.17022	0.738
55DAP/53DAP	1.29894	0.519
57DAP/55DAP	0.87442	0.658
62DAP/57DAP	3.41513	0.303
68DAP/62DAP	1.81402	0.051
68DAP/14DAP	1.99435	0.067

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79489	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.51612
Mature Green Tomato/Ripe Tomato	3.72533	0.016
Immature Eggplant/Mature Eggplant	0.40709
Ripe Pepper/Ripe Tomato	N/A	N/A
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	0.63037
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	3.21596
6-2/M82	7.55403
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	1.14825	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.85816

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	1.07531	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92893	1
DC3000/delta hrp 6h	1.09073	0.777
DC3000/delta hrp 12h	1.22268	1
DC3000/delta hrp 24h	0.88428	0.379

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81893	0.052
DC3000 delta B/DC3000 delta AB	1.01437	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01279	1
Var 0h	1.09531	0.98
Var 12h I row2-row1	0.82993	0.565
Var 12h NI row2-row1	1.43791	0.649
Var 36h I row2-row1	1.46256	0.368
Var 36h NI row2-row1	0.60428	0.478
Var 60h I row2-row1	1.46786	1
Var 60h NI row2-row1	0.74152	0.63
Time course 0hI-0hNI	1.1166	0.833
Time course 12hI-12hNI	0.97409	0.808
Time course 36hI-36hNI	1.92637	0.005
Time course 60hI-60hNI	1.59053	0.096

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)	1.09735	0.654
transgenic ySAMdc/azygous control (breaker)	3.53982	0.248
transgenic ySAMdc/azygous control (red)	0.68827	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00044	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.99665	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.97118	0.083
Manapal/WT (break)	3.24294	0.183
Manapal/WT (red)	0.26903	0.181