Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.11.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00924	0.997
27DAP/17DAP	1.02275	1
39DAP/27DAP	0.97696	0.719
41DAP/39DAP	1.08399	0.252
42DAP/41DAP	0.9132	1
43DAP/42DAP	0.97176	0.864
47DAP/43DAP	0.98393	0.913
52DAP/47DAP	0.97255	0.907
57DAP/52DAP	1.06759	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97199	0.402
17DAP/reference	0.97899	0.597
27DAP/reference	0.9672	0.359
39DAP/reference	0.94523	0.118
41DAP/reference	0.9461	0.039
42DAP/reference	0.96638	0.04
43DAP/reference	0.96963	0.594
47DAP/reference	0.96081	0.174
52DAP/reference	0.93694	0.195
57DAP/reference	1.07706	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99217	0.801
27DAP/17DAP	0.97572	0.887
39DAP/27DAP	0.99964	1
41DAP/39DAP	1.00009	1
42DAP/41DAP	0.97577	0.776
43DAP/42DAP	0.9922	0.928
47DAP/43DAP	1.01723	0.906
52DAP/47DAP	0.99352	0.962
57DAP/52DAP	0.98427	0.763
57DAP/7DAP	0.93187	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88096	0.157
17DAP/reference	0.79404	0.012
27DAP/reference	0.7945	0.01
39DAP/reference	0.88599	0.011
41DAP/reference	0.85679	0.05
42DAP/reference	0.81679	0.021
43DAP/reference	0.76918	0.013
47DAP/reference	0.83496	0.038
52DAP/reference	0.85064	0.031
57DAP/reference	0.8817	0.08

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00934	0.832
17DAP/reference	0.93528	0.058
27DAP/reference	0.99464	0.711
39DAP/reference	0.96057	0.339
41DAP/reference	1.00709	1
42DAP/reference	1.00959	1
43DAP/reference	0.97865	0.592
47DAP/reference	1.0078	1
52DAP/reference	0.95412	0.093
57DAP/reference	1.05833	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79171	0.054
17DAP/reference	0.96302	0.452
27DAP/reference	0.84456	0.028
39DAP/reference	0.76965	0.017
41DAP/reference	0.818	0.032
42DAP/reference	0.75156	0.016
43DAP/reference	0.84001	0.019
47DAP/reference	0.95479	0.215
52DAP/reference	0.8238	0.186
57DAP/reference	0.87492	0.075

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05422	0.945
26DAP/20DAP	1.04017	0.85
34DAP/26DAP	1.03733	1
51DAP/34DAP	1.04383	0.627
52DAP/51DAP	0.95783	1
53DAP/52DAP	1.0192
55DAP/53DAP	1.00866
57DAP/55DAP	0.96832	0.851
62DAP/57DAP	0.9737	0.871
68DAP/62DAP	1.09748	0.523
68DAP/14DAP	1.02175	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96642	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88865
Mature Green Tomato/Ripe Tomato	1.03987	0.898
Immature Eggplant/Mature Eggplant	1.55918	0.248
Ripe Pepper/Ripe Tomato	0.98061
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98745	0.961
1-1-2/M82	1.02891	1
12-2/M82	0.96246	0.955
12-4/M82	0.97839	1
1-3/M82	0.94215	0.501
2-1-1/M82	0.90824	0.465
2-1/M82	N/A	N/A
2-6/M82	0.9087	1
3-2/M82	0.86385	0.752
4-1-1/M82	1.06274	1
4-1/M82	0.995	1
4-3-2/M82	0.89524	1
4-3/M82	0.97814	1
5-3/M82	1.0526	1
6-2/M82	1.02757	1
6-3/M82	0.99477	1
7-1/M82	0.98642	1
7-2/M82	0.95861	0.881
9-3-2/M82	0.86689	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8355	1
IL2-6/WTpooled	1.20601	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.14167	0.362
IL12-4/WTpooled	1.22814	0.538
IL1-4/WTpooled	0.90003
WT/WTpooled	0.95772	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	1.18816	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97378	1
DC3000/delta hrp 6h	1.40554	1
DC3000/delta hrp 12h	0.94385	1
DC3000/delta hrp 24h	1.0681	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07222	0.384
DC3000 delta B/DC3000 delta AB	1.10754	0.345

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.85783	0.699
Exp 60h	0.93385	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98703	1
Var 0h	1.03061	1
Var 12h I row2-row1	1.1812	0.202
Var 12h NI row2-row1	0.9945	1
Var 36h I row2-row1	0.98366	1
Var 36h NI row2-row1	0.74396	1
Var 60h I row2-row1	1.09139	1
Var 60h NI row2-row1	1.07971	1
Time course 0hI-0hNI	1.02684	1
Time course 12hI-12hNI	1.05245	0.746
Time course 36hI-36hNI	1.00904	0.881
Time course 60hI-60hNI	1.49465	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)	0.94852	0.662
transgenic ySAMdc/azygous control (breaker)	1.62539	1
transgenic ySAMdc/azygous control (red)	1.4627	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95896	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10354	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83502	1
Manapal/WT (break)	0.8832	1
Manapal/WT (red)	0.79183	0.181