Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.20.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91644	0.532
27DAP/17DAP	1.29441	0.688
39DAP/27DAP	0.91903	0.583
41DAP/39DAP	1.6527	0.211
42DAP/41DAP	0.9395	1
43DAP/42DAP	0.95076	0.874
47DAP/43DAP	0.97518	0.864
52DAP/47DAP	0.98519	0.934
57DAP/52DAP	0.95594	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96339	0.526
17DAP/reference	1.00495	1
27DAP/reference	0.93386	0.257
39DAP/reference	1.01358	0.747
41DAP/reference	1.0263	0.587
42DAP/reference	0.90017	0.029
43DAP/reference	0.90981	0.346
47DAP/reference	0.96319	0.242
52DAP/reference	0.78835	0.121
57DAP/reference	0.73746	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21725	0.398
27DAP/17DAP	1.08078	0.969
39DAP/27DAP	1.22822	0.46
41DAP/39DAP	0.98388	0.973
42DAP/41DAP	1.31956	0.514
43DAP/42DAP	1.10929	0.699
47DAP/43DAP	0.93195	0.757
52DAP/47DAP	1.11699	0.73
57DAP/52DAP	0.93291	0.628
57DAP/7DAP	1.13755	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2578	0.071
17DAP/reference	1.09726	0.437
27DAP/reference	1.09423	0.107
39DAP/reference	1.23409	0.05
41DAP/reference	1.12178	0.303
42DAP/reference	1.05407	0.889
43DAP/reference	1.63276	0.009
47DAP/reference	1.06932	0.745
52DAP/reference	1.68448	0.011
57DAP/reference	1.52563	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99342	0.869
17DAP/reference	0.91866	0.092
27DAP/reference	0.80065	0.056
39DAP/reference	0.90742	0.25
41DAP/reference	0.8886	0.11
42DAP/reference	0.85539	0.061
43DAP/reference	0.93358	0.344
47DAP/reference	0.90975	0.094
52DAP/reference	1.05382	0.168
57DAP/reference	1.12131	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1057	0.153
17DAP/reference	0.93041	0.313
27DAP/reference	0.99649	0.763
39DAP/reference	1.08089	0.275
41DAP/reference	1.0427	0.754
42DAP/reference	1.19452	0.226
43DAP/reference	1.24223	0.465
47DAP/reference	1.02269	1
52DAP/reference	1.22865	0.393
57DAP/reference	0.63717	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00137	1
26DAP/20DAP	1.42621	0.223
34DAP/26DAP	1.21654	1
51DAP/34DAP	0.91014	0.807
52DAP/51DAP	1.00653	1
53DAP/52DAP	1.00252	0.891
55DAP/53DAP	1.23123	0.927
57DAP/55DAP	0.96781	0.748
62DAP/57DAP	1.19948	0.569
68DAP/62DAP	1.06732	1
68DAP/14DAP	1.026	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09343	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.41035
Mature Green Tomato/Ripe Tomato	0.82174	0.086
Immature Eggplant/Mature Eggplant	1.37646	0.101
Ripe Pepper/Ripe Tomato	0.9742	1
Mature Eggplant/Ripe Tomato	0.79075	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02409	1
1-1-2/M82	0.82068	0.804
12-2/M82	0.87303	0.639
12-4/M82	0.76063	0.619
1-3/M82	3.16063
2-1-1/M82	0.91403	0.92
2-1/M82	0.73293	0.519
2-6/M82	0.99958	1
3-2/M82	1.0857	0.967
4-1-1/M82	1.40952
4-1/M82	1.04605	1
4-3-2/M82	0.94474	1
4-3/M82	1.46134	0.268
5-3/M82	0.92012	0.447
6-2/M82	1.44117
6-3/M82	0.58154
7-1/M82	N/A	N/A
7-2/M82	0.99878	1
9-3-2/M82	0.81551	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99158
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89777
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.95909	0.834
WT/WTpooled	0.95698	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	0.89555	0.032

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82294	1
DC3000/delta hrp 6h	1.2942	1
DC3000/delta hrp 12h	1.06387	1
DC3000/delta hrp 24h	0.93483	0.494

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77639
DC3000 delta B/DC3000 delta AB	1.67851

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11299	1
Exp 36h	1.06324	1
Exp 60h	1.0412	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.90089	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.96783	0.948
Var 12h NI row2-row1	0.87957	0.713
Var 36h I row2-row1	1.37068	0.368
Var 36h NI row2-row1	3.42825	1
Var 60h I row2-row1	0.9094
Var 60h NI row2-row1	0.7542	0.292
Time course 0hI-0hNI	0.83721	0.165
Time course 12hI-12hNI	0.98327	0.964
Time course 36hI-36hNI	0.99064	0.58
Time course 60hI-60hNI	1.24067	0.187

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)	1.31143	0.326
transgenic ySAMdc/azygous control (breaker)	0.62405	0.142
transgenic ySAMdc/azygous control (red)	0.94271	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98418	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92203	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99916	1
Manapal/WT (break)	1.31812	0.381
Manapal/WT (red)	1.11753	1