Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.9.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37756	0.039
27DAP/17DAP	0.62176	0.103
39DAP/27DAP	1.29314	0.444
41DAP/39DAP	0.79034	0.262
42DAP/41DAP	0.97959	1
43DAP/42DAP	1.25763	0.864
47DAP/43DAP	0.47361	0.049
52DAP/47DAP	0.64165	0.201
57DAP/52DAP	0.98935	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32422	0.179
17DAP/reference	1.76128	0.042
27DAP/reference	1.31218	0.111
39DAP/reference	1.34502	0.157
41DAP/reference	1.12653	0.667
42DAP/reference	1.21722	0.076
43DAP/reference	0.81338	0.118
47DAP/reference	0.40139	0.001
52DAP/reference	0.32303	0.012
57DAP/reference	0.58396	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19147	0.348
27DAP/17DAP	0.9785	0.919
39DAP/27DAP	0.67998	0.076
41DAP/39DAP	1.80978	0.748
42DAP/41DAP	0.8761	0.356
43DAP/42DAP	0.65432	0.046
47DAP/43DAP	1.10233	0.529
52DAP/47DAP	0.55468	0.058
57DAP/52DAP	0.81683	0.428
57DAP/7DAP	0.33354	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.26983	0.024
17DAP/reference	1.51601	0.007
27DAP/reference	1.39767	0.02
39DAP/reference	1.56295	0.018
41DAP/reference	1.37417	0.026
42DAP/reference	1.44549	0.018
43DAP/reference	0.95355	0.385
47DAP/reference	1.48716	0.033
52DAP/reference	1.17106	0.266
57DAP/reference	1.32098	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97183	0.655
17DAP/reference	1.93123	0.036
27DAP/reference	1.55573	0.128
39DAP/reference	1.40333	0.016
41DAP/reference	1.2454	0.277
42DAP/reference	1.79854	0.007
43DAP/reference	0.98805	0.298
47DAP/reference	2.01785	0.008
52DAP/reference	0.95749	0.28
57DAP/reference	1.44841	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.17963	0.015
17DAP/reference	2.29424	0.07
27DAP/reference	2.15333	0.012
39DAP/reference	1.88973	0.004
41DAP/reference	1.67411	0.008
42DAP/reference	0.98468	0.816
43DAP/reference	1.23937	0.04
47DAP/reference	0.37846	0.004
52DAP/reference	0.43971	0.052
57DAP/reference	1.01253	0.79

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28869	0.966
26DAP/20DAP	0.85351	1
34DAP/26DAP	1.07865	1
51DAP/34DAP	1.07002	0.927
52DAP/51DAP	1.02463	1
53DAP/52DAP	0.53716
55DAP/53DAP	0.95802	0.686
57DAP/55DAP	0.83029	0.601
62DAP/57DAP	0.92219	0.871
68DAP/62DAP	0.71784	0.505
68DAP/14DAP	0.63392	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.05616	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.34855	0.058
Mature Green Tomato/Ripe Tomato	6.05209	0.015
Immature Eggplant/Mature Eggplant	1.58128	0.054
Ripe Pepper/Ripe Tomato	0.64504	0.224
Mature Eggplant/Ripe Tomato	2.34056	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03531	1
1-1-2/M82	1.12353	1
12-2/M82	0.66896	0.727
12-4/M82	0.73816	0.619
1-3/M82	5.66329	0.26
2-1-1/M82	0.55908
2-1/M82	N/A	N/A
2-6/M82	1.13168	1
3-2/M82	1.11769	1
4-1-1/M82	1.2794	1
4-1/M82	0.84927	1
4-3-2/M82	1.68409	0.508
4-3/M82	1.07017	1
5-3/M82	4.03703	0.427
6-2/M82	4.77751
6-3/M82	1.0345	1
7-1/M82	2.60984	0.741
7-2/M82	3.04266	0.324
9-3-2/M82	3.44564	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.64144	0.277
IL2-6/WTpooled	1.08684	0.584
IL7-5/WTpooled	0.94797	1
IL7-3/WTpooled	0.94528	0.418
IL12-4/WTpooled	1.05183	0.695
IL1-4/WTpooled	2.06166	1
WT/WTpooled	0.96917	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	1.07716	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84017	0.62
DC3000/delta hrp 6h	0.96392	0.95
DC3000/delta hrp 12h	1.35851	1
DC3000/delta hrp 24h	0.94339	0.642

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56683	0.046
DC3000 delta B/DC3000 delta AB	0.45311	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0305	1
Exp 36h	1.0241	1
Exp 60h	0.93283	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97248	1
Var 0h	0.48598	0.933
Var 12h I row2-row1	0.82408	0.363
Var 12h NI row2-row1	0.9521	0.713
Var 36h I row2-row1	0.77243	1
Var 36h NI row2-row1	0.94881	0.706
Var 60h I row2-row1	0.97907	0.952
Var 60h NI row2-row1	1.04446	1
Time course 0hI-0hNI	0.96612	0.817
Time course 12hI-12hNI	1.02093	0.811
Time course 36hI-36hNI	1.06138	0.28
Time course 60hI-60hNI	0.659	0.047

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)	1.12706	0.511
transgenic ySAMdc/azygous control (breaker)	2.54925	0.172
transgenic ySAMdc/azygous control (red)	1.23196	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8178	0.201

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14514	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.2187	0.09
Manapal/WT (break)	6.00047	0.14
Manapal/WT (red)	8.27956	0.15