Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.2.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61482	0.024
27DAP/17DAP	0.71459	0.162
39DAP/27DAP	0.90112	0.573
41DAP/39DAP	1.20392	0.619
42DAP/41DAP	0.77352	0.774
43DAP/42DAP	0.9918	0.937
47DAP/43DAP	1.11535	0.909
52DAP/47DAP	1.19651	0.913
57DAP/52DAP	0.95099	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93163	0.352
17DAP/reference	0.92965	0.26
27DAP/reference	1.05342	0.794
39DAP/reference	1.1846	0.042
41DAP/reference	1.00455	1
42DAP/reference	1.0496	0.504
43DAP/reference	1.0124	0.942
47DAP/reference	1.0534	0.495
52DAP/reference	1.11067	0.272
57DAP/reference	1.09104	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0703	0.858
27DAP/17DAP	0.93453	0.878
39DAP/27DAP	0.75193	0.036
41DAP/39DAP	1.01371	1
42DAP/41DAP	1.04792	1
43DAP/42DAP	0.86765	0.235
47DAP/43DAP	0.94937	0.534
52DAP/47DAP	1.01511	0.979
57DAP/52DAP	1.00475	0.852
57DAP/7DAP	0.79071	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09634	0.344
17DAP/reference	1.12181	0.199
27DAP/reference	1.33511	0.012
39DAP/reference	1.10006	0.411
41DAP/reference	1.34055	0.041
42DAP/reference	1.22736	0.059
43DAP/reference	1.23714	0.06
47DAP/reference	1.08888	0.549
52DAP/reference	1.21888	0.008
57DAP/reference	1.0981	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24454	0.203
17DAP/reference	1.04286	0.904
27DAP/reference	1.25454	0.041
39DAP/reference	1.13528	0.239
41DAP/reference	0.97012	0.441
42DAP/reference	1.28054	0.066
43DAP/reference	1.66537	0.014
47DAP/reference	1.26693	0.032
52DAP/reference	1.20652	0.03
57DAP/reference	0.87447	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01761	1
17DAP/reference	1.13411	0.14
27DAP/reference	1.26632	0.03
39DAP/reference	1.16997	0.13
41DAP/reference	1.15759	0.077
42DAP/reference	1.05325	0.6
43DAP/reference	1.08735	0.565
47DAP/reference	1.0386	0.667
52DAP/reference	1.0601	0.851
57DAP/reference	1.24369	0.072

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35235	0.752
26DAP/20DAP	1.23333	0.366
34DAP/26DAP	0.72022	0.092
51DAP/34DAP	0.63067	0.056
52DAP/51DAP	0.94487	1
53DAP/52DAP	0.69751	0.186
55DAP/53DAP	0.85908	0.376
57DAP/55DAP	0.95257	0.821
62DAP/57DAP	0.72173
68DAP/62DAP	1.36931	0.185
68DAP/14DAP	1.4103	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96005	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.29309	0.058
Mature Green Tomato/Ripe Tomato	0.81695	0.411
Immature Eggplant/Mature Eggplant	1.08665	0.222
Ripe Pepper/Ripe Tomato	0.93307	1
Mature Eggplant/Ripe Tomato	1.08305	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93669	0.944
1-1-2/M82	1.08988	1
12-2/M82	1.25624
12-4/M82	1.06674	1
1-3/M82	0.84065
2-1-1/M82	0.89886	0.465
2-1/M82	1.35991	0.345
2-6/M82	1.21878	0.695
3-2/M82	0.96437
4-1-1/M82	1.13483	1
4-1/M82	N/A	N/A
4-3-2/M82	1.29937	0.508
4-3/M82	0.94867	1
5-3/M82	0.92691	0.642
6-2/M82	0.86006
6-3/M82	1.08333	1
7-1/M82	1.08399	1
7-2/M82	0.95423	0.881
9-3-2/M82	1.31499

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61093
IL2-6/WTpooled	0.88454	0.473
IL7-5/WTpooled	1.29087
IL7-3/WTpooled	1.19124	0.362
IL12-4/WTpooled	1.12881	0.695
IL1-4/WTpooled	0.94403	0.834
WT/WTpooled	0.98576	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	0.91341	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.23016	0.715
DC3000/delta hrp 6h	1.00232	0.95
DC3000/delta hrp 12h	0.90996	1
DC3000/delta hrp 24h	1.00438	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54262	0.025
DC3000 delta B/DC3000 delta AB	0.36254	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82576	1
Exp 36h	0.86556	0.82
Exp 60h	0.90308	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9697	1
Var 0h	0.54126	0.933
Var 12h I row2-row1	0.76513	0.357
Var 12h NI row2-row1	0.98027	0.906
Var 36h I row2-row1	0.9426	1
Var 36h NI row2-row1	1.23026	0.482
Var 60h I row2-row1	1.42945	0.562
Var 60h NI row2-row1	1.063	1
Time course 0hI-0hNI	0.97821	0.922
Time course 12hI-12hNI	0.9371	0.357
Time course 36hI-36hNI	0.82198	0.048
Time course 60hI-60hNI	0.15928	0.005

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)	1.00616	0.654
transgenic ySAMdc/azygous control (breaker)	0.79283	0.139
transgenic ySAMdc/azygous control (red)	0.92098	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99713	0.858

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98935	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05938	1
Manapal/WT (break)	1.45996	0.381
Manapal/WT (red)	0.69577	0.188