Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04165	0.964
27DAP/17DAP	0.80767	0.381
39DAP/27DAP	0.83472	0.421
41DAP/39DAP	1.3331	0.227
42DAP/41DAP	1.23574	0.825
43DAP/42DAP	0.95836	0.827
47DAP/43DAP	0.96999	0.864
52DAP/47DAP	1.55272	0.238
57DAP/52DAP	0.88337	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18518	0.147
17DAP/reference	0.99405	0.957
27DAP/reference	0.97982	0.711
39DAP/reference	1.0777	0.359
41DAP/reference	1.19889	0.287
42DAP/reference	1.22372	0.21
43DAP/reference	1.14526	0.118
47DAP/reference	1.11195	0.306
52DAP/reference	1.12708	0.195
57DAP/reference	0.77641	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05333	0.536
27DAP/17DAP	0.92818	0.58
39DAP/27DAP	1.11279	0.496
41DAP/39DAP	1.06019	0.883
42DAP/41DAP	1.01289	1
43DAP/42DAP	0.99991	1
47DAP/43DAP	0.99034	0.954
52DAP/47DAP	1.04765	0.823
57DAP/52DAP	1.0495	0.718
57DAP/7DAP	1.17811	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89594	0.108
17DAP/reference	0.83233	0.013
27DAP/reference	0.87014	0.01
39DAP/reference	0.84074	0.011
41DAP/reference	0.85457	0.016
42DAP/reference	0.80848	0.01
43DAP/reference	0.88171	0.029
47DAP/reference	0.87896	0.101
52DAP/reference	0.83764	0.02
57DAP/reference	0.82177	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20539	0.05
17DAP/reference	1.1617	0.05
27DAP/reference	1.13251	0.225
39DAP/reference	1.14164	0.103
41DAP/reference	1.08369	0.831
42DAP/reference	1.05905	0.715
43DAP/reference	1.30453	0.103
47DAP/reference	0.89596	0.049
52DAP/reference	1.15768	0.012
57DAP/reference	1.21606	0.042

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84459	0.071
17DAP/reference	1.01581	0.956
27DAP/reference	0.83479	0.024
39DAP/reference	0.8469	0.013
41DAP/reference	1.001	0.826
42DAP/reference	0.97347	0.671
43DAP/reference	0.96915	0.484
47DAP/reference	0.97828	0.538
52DAP/reference	0.92145	0.395
57DAP/reference	1.09533	0.371

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10818	0.966
26DAP/20DAP	0.91735	0.512
34DAP/26DAP	1.0534	0.819
51DAP/34DAP	1.06154	0.666
52DAP/51DAP	1.06785	0.232
53DAP/52DAP	1.01992	0.882
55DAP/53DAP	1.00126	0.951
57DAP/55DAP	0.98252	0.911
62DAP/57DAP	1.30914	0.622
68DAP/62DAP	0.81316	0.378
68DAP/14DAP	0.91556	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15701	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96749	0.635
Mature Green Tomato/Ripe Tomato	1.01092	0.774
Immature Eggplant/Mature Eggplant	0.9003	0.117
Ripe Pepper/Ripe Tomato	0.95382	1
Mature Eggplant/Ripe Tomato	0.51068	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99167	0.961
1-1-2/M82	N/A	N/A
12-2/M82	1.28892	1
12-4/M82	0.93202	1
1-3/M82	1.0547
2-1-1/M82	1.06513
2-1/M82	0.92104
2-6/M82	1.04275	1
3-2/M82	N/A	N/A
4-1-1/M82	1.08807	1
4-1/M82	0.94498	1
4-3-2/M82	1.26668
4-3/M82	1.08842	1
5-3/M82	0.916	0.49
6-2/M82	0.90576
6-3/M82	0.84097
7-1/M82	N/A	N/A
7-2/M82	1.03318	1
9-3-2/M82	0.88158	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04166	1
IL2-6/WTpooled	1.39869	0.584
IL7-5/WTpooled	1.21163	0.792
IL7-3/WTpooled	0.66171	0.31
IL12-4/WTpooled	0.94799	1
IL1-4/WTpooled	1.07782	1
WT/WTpooled	0.92967	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	0.86471	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03244	0.875
DC3000/delta hrp 6h	0.98312	0.95
DC3000/delta hrp 12h	1.01198	1
DC3000/delta hrp 24h	1.00066	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90017	0.365
DC3000 delta B/DC3000 delta AB	0.97296	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.71087	1
Exp 36h	0.68124	0.406
Exp 60h	0.64387	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97513	1
Var 0h	0.97103	1
Var 12h I row2-row1	0.96883	0.39
Var 12h NI row2-row1	1.16063	0.649
Var 36h I row2-row1	0.95442	0.805
Var 36h NI row2-row1	1.01599	1
Var 60h I row2-row1	1.46847	1
Var 60h NI row2-row1	1.0333	0.904
Time course 0hI-0hNI	0.95446	0.56
Time course 12hI-12hNI	1.0093	0.854
Time course 36hI-36hNI	0.92187	0.084
Time course 60hI-60hNI	0.50461	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)	1.14259	0.294
transgenic ySAMdc/azygous control (breaker)	1.0299	1
transgenic ySAMdc/azygous control (red)	1.02518	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02746	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42148	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.5008	0.14
Manapal/WT (break)	1.82335	0.13
Manapal/WT (red)	1.03658	1