Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.10.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37598	0.67
27DAP/17DAP	0.94485	0.81
39DAP/27DAP	1.09929	0.888
41DAP/39DAP	0.8324	0.35
42DAP/41DAP	0.7856	0.774
43DAP/42DAP	0.90539	0.801
47DAP/43DAP	0.90704	0.687
52DAP/47DAP	0.68361	0.33
57DAP/52DAP	0.83385	0.836

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96787	0.465
17DAP/reference	1.2549	0.049
27DAP/reference	1.62804	0.007
39DAP/reference	1.33979	0.077
41DAP/reference	1.25681	0.021
42DAP/reference	0.91114	0.02
43DAP/reference	0.97381	0.653
47DAP/reference	0.95713	0.279
52DAP/reference	0.90905	0.215
57DAP/reference	1.09189	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11051	0.356
27DAP/17DAP	1.17956	0.383
39DAP/27DAP	1.08366	0.56
41DAP/39DAP	1.07031	0.817
42DAP/41DAP	1.05115	0.886
43DAP/42DAP	0.62599	0.022
47DAP/43DAP	1.03405	0.756
52DAP/47DAP	0.9169	0.686
57DAP/52DAP	0.85967	0.211
57DAP/7DAP	0.74206	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29948	0.091
17DAP/reference	1.62136	0.01
27DAP/reference	1.32561	0.011
39DAP/reference	1.31063	0.042
41DAP/reference	1.23868	0.147
42DAP/reference	1.45284	0.007
43DAP/reference	1.14517	0.148
47DAP/reference	1.11473	0.468
52DAP/reference	1.40314	0.01
57DAP/reference	0.99385	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04927	0.695
17DAP/reference	1.16628	0.079
27DAP/reference	1.21968	0.107
39DAP/reference	1.36669	0.014
41DAP/reference	1.03671	1
42DAP/reference	1.40384	0.022
43DAP/reference	1.31491	0.146
47DAP/reference	1.06535	1
52DAP/reference	1.1712	0.393
57DAP/reference	1.15702	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16027	0.258
17DAP/reference	1.1011	0.814
27DAP/reference	1.91969	0.016
39DAP/reference	1.50639	0.008
41DAP/reference	1.3352	0.05
42DAP/reference	1.44637	0.04
43DAP/reference	1.10657	0.744
47DAP/reference	0.85303	0.183
52DAP/reference	1.12451	0.428
57DAP/reference	0.87074	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15112	0.966
26DAP/20DAP	1.45583	0.152
34DAP/26DAP	0.84064	0.627
51DAP/34DAP	0.63768	0.059
52DAP/51DAP	0.89245	1
53DAP/52DAP	0.97511	0.876
55DAP/53DAP	0.47303	0.016
57DAP/55DAP	0.88936	0.587
62DAP/57DAP	0.90506	0.871
68DAP/62DAP	0.94936	0.787
68DAP/14DAP	0.64329

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.94748	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	10.8202	0.058
Mature Green Tomato/Ripe Tomato	4.49684	0.022
Immature Eggplant/Mature Eggplant	0.9702	0.808
Ripe Pepper/Ripe Tomato	0.82539	1
Mature Eggplant/Ripe Tomato	3.91781	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22947	0.877
1-1-2/M82	1.01569	1
12-2/M82	0.8396
12-4/M82	1.01426	1
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	1.00456	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	0.90182
4-3/M82	N/A	N/A
5-3/M82	1.02193	0.467
6-2/M82	2.25312
6-3/M82	0.98112	1
7-1/M82	N/A	N/A
7-2/M82	1.3871
9-3-2/M82	1.07611	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9981
IL2-6/WTpooled	0.90129	0.348
IL7-5/WTpooled	3.08648
IL7-3/WTpooled	0.96388	1
IL12-4/WTpooled	0.86809
IL1-4/WTpooled	1.07933	0.426
WT/WTpooled	0.77162	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	1.02662	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98733	1
DC3000/delta hrp 6h	1.25521	1
DC3000/delta hrp 12h	1.00127	1
DC3000/delta hrp 24h	0.65906	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01742	1
DC3000 delta B/DC3000 delta AB	1.42832	0.159

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96874	1
Exp 36h	0.79606	0.471
Exp 60h	0.98611	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03203	1
Var 0h	1.19518	0.936
Var 12h I row2-row1	1.0044	1
Var 12h NI row2-row1	1.10105	0.649
Var 36h I row2-row1	0.81413	1
Var 36h NI row2-row1	0.99297	0.852
Var 60h I row2-row1	0.78088	0.374
Var 60h NI row2-row1	1.06809	0.904
Time course 0hI-0hNI	1.00399	1
Time course 12hI-12hNI	0.9743	0.827
Time course 36hI-36hNI	0.91347	0.29
Time course 60hI-60hNI	1.06175	0.426

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)	0.92321	0.529
transgenic ySAMdc/azygous control (breaker)	1.00401	1
transgenic ySAMdc/azygous control (red)	0.88814	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1814	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33588	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76173	0.172
Manapal/WT (break)	1.11978	1
Manapal/WT (red)	0.80705	0.315