Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9488	0.671
27DAP/17DAP	1.26199	0.732
39DAP/27DAP	0.86598	0.399
41DAP/39DAP	1.17967	0.298
42DAP/41DAP	0.87784	1
43DAP/42DAP	0.96828	0.877
47DAP/43DAP	0.99944	0.953
52DAP/47DAP	0.80148	0.471
57DAP/52DAP	1.12702	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76929	0.049
17DAP/reference	0.81494	0.011
27DAP/reference	0.88279	0.07
39DAP/reference	0.9063	0.174
41DAP/reference	0.67953	0.008
42DAP/reference	0.79892	0.002
43DAP/reference	0.90979	0.148
47DAP/reference	0.87618	0.116
52DAP/reference	1.15477	0.167
57DAP/reference	1.29328	0.021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88465	0.336
27DAP/17DAP	1.09158	0.694
39DAP/27DAP	1.05348	0.677
41DAP/39DAP	0.93955	0.696
42DAP/41DAP	0.99935	0.887
43DAP/42DAP	1.12131	0.192
47DAP/43DAP	1.03206	0.837
52DAP/47DAP	0.9547	0.797
57DAP/52DAP	0.97477	0.745
57DAP/7DAP	1.00354	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30351	0.035
17DAP/reference	1.17272	0.064
27DAP/reference	1.08455	0.974
39DAP/reference	1.17791	0.044
41DAP/reference	1.2014	0.46
42DAP/reference	0.98484	0.554
43DAP/reference	1.15751	0.083
47DAP/reference	0.97842	0.671
52DAP/reference	0.8445	0.278
57DAP/reference	0.99868	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79919	0.016
17DAP/reference	0.72268	0.01
27DAP/reference	0.75783	0.021
39DAP/reference	0.90349	0.156
41DAP/reference	0.95628	0.242
42DAP/reference	0.88672	0.108
43DAP/reference	0.68191	0.003
47DAP/reference	0.87643	0.099
52DAP/reference	0.88857	0.01
57DAP/reference	0.7369	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1207	0.287
17DAP/reference	0.98686	0.727
27DAP/reference	1.20189	0.03
39DAP/reference	1.08877	0.563
41DAP/reference	0.99205	0.682
42DAP/reference	1.01456	1
43DAP/reference	1.01414	0.858
47DAP/reference	0.97689	0.509
52DAP/reference	2.8506	0.289
57DAP/reference	1.40093	0.094

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12211	0.966
26DAP/20DAP	1.18767	0.594
34DAP/26DAP	0.98104	0.988
51DAP/34DAP	1.21817	0.159
52DAP/51DAP	0.93596	1
53DAP/52DAP	1.00237	1
55DAP/53DAP	0.84465	0.163
57DAP/55DAP	1.06769	0.969
62DAP/57DAP	0.79951	0.28
68DAP/62DAP	1.45838	0.124
68DAP/14DAP	1.51079	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77141	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80453	0.276
Mature Green Tomato/Ripe Tomato	0.91698	0.611
Immature Eggplant/Mature Eggplant	1.05621	0.659
Ripe Pepper/Ripe Tomato	1.48778	0.256
Mature Eggplant/Ripe Tomato	0.96348	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97992	0.961
1-1-2/M82	1.0926	1
12-2/M82	0.95616	0.955
12-4/M82	0.83879	0.619
1-3/M82	0.99919
2-1-1/M82	1.08659	0.764
2-1/M82	1.19375	1
2-6/M82	1.06262	1
3-2/M82	1.03555	0.967
4-1-1/M82	1.05546	1
4-1/M82	0.89607	1
4-3-2/M82	0.94267	1
4-3/M82	1.05214	1
5-3/M82	1.13837	0.496
6-2/M82	0.87451	1
6-3/M82	1.02801	1
7-1/M82	0.82051	0.509
7-2/M82	1.41303	0.385
9-3-2/M82	1.07968	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94011	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.92796	1
IL12-4/WTpooled	1.12245	0.737
IL1-4/WTpooled	1.07963	1
WT/WTpooled	0.96028	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	1.54673	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07389	0.921
DC3000/delta hrp 6h	0.97975	0.95
DC3000/delta hrp 12h	1.02795	1
DC3000/delta hrp 24h	1.24393	0.118

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52993	0.042
DC3000 delta B/DC3000 delta AB	1.51843	0.101

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96224	1
Exp 36h	1.07248	1
Exp 60h	1.26371	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07103	1
Var 0h	0.99249	1
Var 12h I row2-row1	1.1006	0.692
Var 12h NI row2-row1	1.11103	1
Var 36h I row2-row1	1.1767	0.305
Var 36h NI row2-row1	0.76018	0.225
Var 60h I row2-row1	0.75707	0.306
Var 60h NI row2-row1	0.93008	0.516
Time course 0hI-0hNI	1.02254	0.852
Time course 12hI-12hNI	0.99863	1
Time course 36hI-36hNI	1.33341	0.005
Time course 60hI-60hNI	2.92736	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)	0.97443	0.428
transgenic ySAMdc/azygous control (breaker)	1.24657	0.172
transgenic ySAMdc/azygous control (red)	1.05824	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95961	0.153

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76368	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07313	1
Manapal/WT (break)	0.89063	1
Manapal/WT (red)	0.67597	0.181