Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15723	0.477
27DAP/17DAP	0.65263	0.121
39DAP/27DAP	1.05655	0.972
41DAP/39DAP	0.95795	0.824
42DAP/41DAP	0.83156	0.774
43DAP/42DAP	0.99079	0.937
47DAP/43DAP	0.95971	0.84
52DAP/47DAP	1.32797	0.446
57DAP/52DAP	0.91094	0.903

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0301	0.9
17DAP/reference	1.07297	0.172
27DAP/reference	1.01018	0.953
39DAP/reference	1.08243	0.262
41DAP/reference	1.05677	0.667
42DAP/reference	0.93439	0.043
43DAP/reference	1.01487	0.866
47DAP/reference	0.93142	0.05
52DAP/reference	0.8782	0.096
57DAP/reference	0.83261	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21303	0.105
27DAP/17DAP	0.95993	0.878
39DAP/27DAP	0.95847	0.45
41DAP/39DAP	1.00046	1
42DAP/41DAP	1.00562	1
43DAP/42DAP	1.00737	0.83
47DAP/43DAP	1.01776	0.873
52DAP/47DAP	1.04533	0.892
57DAP/52DAP	1.05484	0.763
57DAP/7DAP	1.03116	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84035	0.088
17DAP/reference	0.88254	0.044
27DAP/reference	0.90203	0.071
39DAP/reference	0.94398	0.014
41DAP/reference	0.86525	0.009
42DAP/reference	0.90492	0.014
43DAP/reference	0.81333	0.013
47DAP/reference	0.83441	0.079
52DAP/reference	0.73559	0.031
57DAP/reference	0.83975	0.041

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10547	0.501
17DAP/reference	1.0012	0.873
27DAP/reference	0.92857	0.173
39DAP/reference	0.99018	0.586
41DAP/reference	0.92352	0.177
42DAP/reference	0.90209	0.012
43DAP/reference	1.01534	0.929
47DAP/reference	0.96774	0.328
52DAP/reference	1.00122	0.761
57DAP/reference	1.09824	0.269

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92198	0.077
17DAP/reference	0.9732	0.508
27DAP/reference	0.91041	0.046
39DAP/reference	0.88999	0.022
41DAP/reference	0.89103	0.035
42DAP/reference	0.83195	0.049
43DAP/reference	0.89527	0.267
47DAP/reference	0.921	0.224
52DAP/reference	0.86756	0.125
57DAP/reference	0.68261	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94917	0.961
26DAP/20DAP	1.01182	1
34DAP/26DAP	0.91674	0.642
51DAP/34DAP	0.72837	0.057
52DAP/51DAP	1.01087	0.965
53DAP/52DAP	0.99001	0.96
55DAP/53DAP	0.97207	0.796
57DAP/55DAP	0.92923	0.736
62DAP/57DAP	1.19819	0.678
68DAP/62DAP	1.00595	0.885
68DAP/14DAP	0.80141	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88927	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.43524	0.113
Mature Green Tomato/Ripe Tomato	1.53221	0.053
Immature Eggplant/Mature Eggplant	1.23484	0.081
Ripe Pepper/Ripe Tomato	0.46741	0.224
Mature Eggplant/Ripe Tomato	0.96579	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18943	0.877
1-1-2/M82	0.95449	1
12-2/M82	1.15596	1
12-4/M82	0.84287	0.619
1-3/M82	0.95288	0.441
2-1-1/M82	1.10805
2-1/M82	1.188	1
2-6/M82	1.00321	1
3-2/M82	0.85735
4-1-1/M82	0.90081	0.962
4-1/M82	0.97301	1
4-3-2/M82	0.99243	1
4-3/M82	1.00693	1
5-3/M82	0.88998	0.49
6-2/M82	0.91844	1
6-3/M82	1.00188	1
7-1/M82	0.77887	0.803
7-2/M82	0.8549	0.796
9-3-2/M82	1.11329	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82688
IL2-6/WTpooled	1.07629	1
IL7-5/WTpooled	0.83829
IL7-3/WTpooled	0.93041	1
IL12-4/WTpooled	1.09227	0.646
IL1-4/WTpooled	0.93137	0.415
WT/WTpooled	0.99753	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	0.87615	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98969	1
DC3000/delta hrp 6h	0.9728	0.95
DC3000/delta hrp 12h	0.98938	1
DC3000/delta hrp 24h	1.19807	0.074

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57758	0.031
DC3000 delta B/DC3000 delta AB	0.54942	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19725	1
Exp 36h	0.78252	0.589
Exp 60h	0.58138	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9932	1
Var 0h	1.01248	1
Var 12h I row2-row1	0.90917	0.627
Var 12h NI row2-row1	0.9531	0.627
Var 36h I row2-row1	0.92195	0.805
Var 36h NI row2-row1	1.05459	1
Var 60h I row2-row1	1.53524	0.562
Var 60h NI row2-row1	1.04011	0.904
Time course 0hI-0hNI	1.02309	0.833
Time course 12hI-12hNI	1.01133	0.85
Time course 36hI-36hNI	1.00195	0.783
Time course 60hI-60hNI	0.2975	0.006

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)	0.90263	0.314
transgenic ySAMdc/azygous control (breaker)	0.77644	0.173
transgenic ySAMdc/azygous control (red)	1.08918	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01345	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95346	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39178	0.09
Manapal/WT (break)	0.69894	0.333
Manapal/WT (red)	0.68462	0.184