Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.975	0.689
27DAP/17DAP	1.01643	0.992
39DAP/27DAP	1.22946	0.497
41DAP/39DAP	1.14706	0.422
42DAP/41DAP	1.07743	0.978
43DAP/42DAP	0.91536	0.788
47DAP/43DAP	1.05511	0.873
52DAP/47DAP	0.72302	0.325
57DAP/52DAP	1.18025	0.771

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78372	0.071
17DAP/reference	0.82898	0.024
27DAP/reference	0.90989	0.223
39DAP/reference	0.8482	0.062
41DAP/reference	0.70207	0.009
42DAP/reference	0.78016	0.013
43DAP/reference	0.93944	0.17
47DAP/reference	0.89083	0.191
52DAP/reference	1.02613	1
57DAP/reference	1.16529	0.202

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15196	0.762
27DAP/17DAP	1.17938	0.557
39DAP/27DAP	1.04303	0.718
41DAP/39DAP	0.94908	0.885
42DAP/41DAP	0.90592	0.42
43DAP/42DAP	1.35261	0.021
47DAP/43DAP	1.13316	0.406
52DAP/47DAP	1.15029	0.586
57DAP/52DAP	1.10508	0.407
57DAP/7DAP	1.21095	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.85704	0.054
17DAP/reference	3.58044	0.006
27DAP/reference	3.60866	0.006
39DAP/reference	5.07392	0.005
41DAP/reference	4.79513	0.011
42DAP/reference	5.58763	0.006
43DAP/reference	5.82127	0.007
47DAP/reference	2.63918	0.158
52DAP/reference	4.31347	0.007
57DAP/reference	3.23755	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8333	0.182
17DAP/reference	0.70513	0.009
27DAP/reference	0.79912	0.017
39DAP/reference	0.83526	0.047
41DAP/reference	0.89519	0.115
42DAP/reference	0.85152	0.055
43DAP/reference	0.63365	0.019
47DAP/reference	0.79907	0.051
52DAP/reference	0.78905	0.007
57DAP/reference	0.65557	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.81649	0.019
17DAP/reference	1.79335	0.427
27DAP/reference	3.38945	0.018
39DAP/reference	2.75886	0.026
41DAP/reference	2.92121	0.01
42DAP/reference	2.86927	0.032
43DAP/reference	2.86842	0.022
47DAP/reference	0.93663	0.168
52DAP/reference	4.11355	0.082
57DAP/reference	2.13927	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31646	0.966
26DAP/20DAP	1.1824	0.608
34DAP/26DAP	0.98069	0.98
51DAP/34DAP	1.49992	0.044
52DAP/51DAP	0.80193	0.151
53DAP/52DAP	0.86716	0.202
55DAP/53DAP	0.81114	0.098
57DAP/55DAP	0.99548	0.93
62DAP/57DAP	1.13524	0.678
68DAP/62DAP	1.6154	0.079
68DAP/14DAP	2.36176	0.036

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8871	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.31136	0.03
Immature Eggplant/Mature Eggplant	1.80243
Ripe Pepper/Ripe Tomato	0.27382
Mature Eggplant/Ripe Tomato	3.62501	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.53288
12-2/M82	N/A	N/A
12-4/M82	0.89301
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	N/A	N/A
3-2/M82	0.75883
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.17513
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.8746
7-1/M82	N/A	N/A
7-2/M82	0.73869
9-3-2/M82	1.09097	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.63801	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.3604	1
IL12-4/WTpooled	1.0041	1
IL1-4/WTpooled	1.3201
WT/WTpooled	0.99897	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	0.96794	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89464	0.697
DC3000/delta hrp 6h	1.12601	1
DC3000/delta hrp 12h	0.81267	1
DC3000/delta hrp 24h	0.61997	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44409
DC3000 delta B/DC3000 delta AB	1.71364

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98727	1
Exp 36h	0.94309	0.943
Exp 60h	0.76077	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05539	1
Var 0h	0.56234	0.936
Var 12h I row2-row1	1.11809	0.283
Var 12h NI row2-row1	1.14232	0.649
Var 36h I row2-row1	0.8095	1
Var 36h NI row2-row1	1.04708	1
Var 60h I row2-row1	0.8356	0.832
Var 60h NI row2-row1	0.91696	0.932
Time course 0hI-0hNI	0.99106	0.991
Time course 12hI-12hNI	1.34286	0.022
Time course 36hI-36hNI	1.38096	0.005
Time course 60hI-60hNI	1.63256	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)	1.28267	0.331
transgenic ySAMdc/azygous control (breaker)	0.42047	0.131
transgenic ySAMdc/azygous control (red)	1.07947	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92778	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69511	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96521	1
Manapal/WT (break)	1.20903	0.381
Manapal/WT (red)	1.06427	0.863