Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00035	0.858
27DAP/17DAP	1.03448	0.984
39DAP/27DAP	1.0683	1
41DAP/39DAP	1.16147	0.85
42DAP/41DAP	1.24842	0.912
43DAP/42DAP	0.81156	0.708
47DAP/43DAP	1.43017	0.746
52DAP/47DAP	1.93846	0.198
57DAP/52DAP	1.05882	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80058	0.145
17DAP/reference	0.62516	0.009
27DAP/reference	0.74879	0.17
39DAP/reference	0.65471	0.011
41DAP/reference	0.55347	0.013
42DAP/reference	0.73461	0.001
43DAP/reference	1.08	0.82
47DAP/reference	0.82295	0.055
52DAP/reference	1.04296	0.121
57DAP/reference	0.51657

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99671	0.871
27DAP/17DAP	1.10584	0.826
39DAP/27DAP	0.94918	0.607
41DAP/39DAP	1.00041	1
42DAP/41DAP	1.0034	0.913
43DAP/42DAP	1.0329	0.699
47DAP/43DAP	0.90645	0.439
52DAP/47DAP	1.54299	0.106
57DAP/52DAP	1.45655	0.093
57DAP/7DAP	1.23021	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88055	0.146
17DAP/reference	0.93359	0.019
27DAP/reference	0.8941	0.011
39DAP/reference	0.88211	0.039
41DAP/reference	0.90354	0.016
42DAP/reference	0.90354	0.017
43DAP/reference	0.9385	0.175
47DAP/reference	0.97643	0.671
52DAP/reference	0.83087	0.01
57DAP/reference	0.94758	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88223	0.124
17DAP/reference	0.85212	0.049
27DAP/reference	0.99679	0.711
39DAP/reference	1.0078	0.702
41DAP/reference	1.03227	1
42DAP/reference	0.96604	0.392
43DAP/reference	0.73767	0.062
47DAP/reference	0.78741	0.015
52DAP/reference	0.89026	0.078
57DAP/reference	0.79263	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87012	0.169
17DAP/reference	0.95914	0.636
27DAP/reference	1.02638	0.621
39DAP/reference	0.9169	0.031
41DAP/reference	0.95464	0.331
42DAP/reference	1.13507	0.789
43DAP/reference	1.14257	0.515
47DAP/reference	0.95543	0.421
52DAP/reference	0.88136	0.184
57DAP/reference	1.65243	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12687	0.966
26DAP/20DAP	1.1381	0.941
34DAP/26DAP	2.00665	0.819
51DAP/34DAP	0.88302	0.563
52DAP/51DAP	2.29656	0.051
53DAP/52DAP	0.79114	0.087
55DAP/53DAP	1.62804	0.039
57DAP/55DAP	0.56605	0.066
62DAP/57DAP	1.07545	0.445
68DAP/62DAP	1.90165	0.398
68DAP/14DAP	2.76847	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65227	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77978	0.234
Mature Green Tomato/Ripe Tomato	0.66906	0.017
Immature Eggplant/Mature Eggplant	0.67614	0.077
Ripe Pepper/Ripe Tomato	2.29414	0.258
Mature Eggplant/Ripe Tomato	0.67264	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75479	0.548
1-1-2/M82	1.11533	1
12-2/M82	0.94981	0.955
12-4/M82	0.79748	0.319
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	1.00612	1
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	1.44686
5-3/M82	1.07831	1
6-2/M82	N/A	N/A
6-3/M82	1.03615	1
7-1/M82	N/A	N/A
7-2/M82	0.92376	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.58261	0.243
IL2-6/WTpooled	0.96801	1
IL7-5/WTpooled	0.98885	1
IL7-3/WTpooled	0.48323	0.294
IL12-4/WTpooled	0.91397	1
IL1-4/WTpooled	0.76812	0.444
WT/WTpooled	1.0696	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	1.0117	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01233	0.921
DC3000/delta hrp 6h	1.03003	1
DC3000/delta hrp 12h	1.09419	1
DC3000/delta hrp 24h	0.9701	0.818

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18777	0.229
DC3000 delta B/DC3000 delta AB	1.16571	0.321

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89716	0.213
Exp 36h	0.96327	0.943
Exp 60h	1.16357	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.81074
Var 0h	0.93703	0.98
Var 12h I row2-row1	0.7935	0.467
Var 12h NI row2-row1	1.22912	0.649
Var 36h I row2-row1	0.91445	1
Var 36h NI row2-row1	0.98814	0.852
Var 60h I row2-row1	0.88568	0.832
Var 60h NI row2-row1	0.94107	0.977
Time course 0hI-0hNI	1.01868	0.852
Time course 12hI-12hNI	1.00095	1
Time course 36hI-36hNI	1.07888	0.063
Time course 60hI-60hNI	0.83231	0.081

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)	1.01637	0.455
transgenic ySAMdc/azygous control (breaker)	1.95233	0.172
transgenic ySAMdc/azygous control (red)	1.23701	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04393	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17081	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10954	1
Manapal/WT (break)	1.39384	0.381
Manapal/WT (red)	1.68983	0.126