Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.10.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79269	0.162
27DAP/17DAP	0.79163	0.451
39DAP/27DAP	0.77026	0.512
41DAP/39DAP	1.51903	0.612
42DAP/41DAP	1.01467	1
43DAP/42DAP	1.30186	0.662
47DAP/43DAP	0.83449	0.496
52DAP/47DAP	1.12094	0.819
57DAP/52DAP	1.01351	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06492	0.638
17DAP/reference	0.99744	0.957
27DAP/reference	0.95906	0.484
39DAP/reference	0.96272	0.565
41DAP/reference	0.82809	0.026
42DAP/reference	0.84945	0.035
43DAP/reference	0.92502	0.071
47DAP/reference	0.79747	0.077
52DAP/reference	0.99277	0.58
57DAP/reference	0.9987	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19104	0.464
27DAP/17DAP	0.7199	0.172
39DAP/27DAP	0.80231	0.316
41DAP/39DAP	1.0684	0.849
42DAP/41DAP	0.8017	0.379
43DAP/42DAP	0.85356	0.082
47DAP/43DAP	1.23186	0.147
52DAP/47DAP	1.24122	0.593
57DAP/52DAP	0.95573	0.7
57DAP/7DAP	0.59446	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18773	0.154
17DAP/reference	1.28532	0.035
27DAP/reference	1.10472	0.453
39DAP/reference	0.98088	0.552
41DAP/reference	0.92832	0.375
42DAP/reference	0.95823	0.393
43DAP/reference	0.9584	0.385
47DAP/reference	1.05904	0.822
52DAP/reference	0.90125	0.126
57DAP/reference	0.99886	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94627	0.564
17DAP/reference	1.13402	0.285
27DAP/reference	0.98777	0.619
39DAP/reference	0.97452	0.509
41DAP/reference	1.00324	0.631
42DAP/reference	0.96996	0.534
43DAP/reference	1.08223	0.761
47DAP/reference	0.88529	0.028
52DAP/reference	0.99939	0.666
57DAP/reference	1.02935	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69108	0.016
17DAP/reference	1.17025	0.462
27DAP/reference	1.12347	0.284
39DAP/reference	1.21249	0.048
41DAP/reference	1.11697	0.239
42DAP/reference	1.06038	0.802
43DAP/reference	1.13241	0.237
47DAP/reference	1.10411	0.265
52DAP/reference	0.91733	0.424
57DAP/reference	1.14947	0.063

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.36803	0.966
26DAP/20DAP	1.2595	0.481
34DAP/26DAP	0.9611	0.795
51DAP/34DAP	0.8836	0.328
52DAP/51DAP	1.24883	0.842
53DAP/52DAP	0.83215	0.435
55DAP/53DAP	1.48677	0.494
57DAP/55DAP	0.93031	0.56
62DAP/57DAP	0.79785	0.28
68DAP/62DAP	1.50859	0.664
68DAP/14DAP	1.50787	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70004	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.89223	1
Mature Green Tomato/Ripe Tomato	8.42626	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.05165
12-2/M82	1.1297
12-4/M82	1.0658
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	0.64883
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1646	0.365
IL2-6/WTpooled	1.02117	1
IL7-5/WTpooled	0.83239	1
IL7-3/WTpooled	1.0805	1
IL12-4/WTpooled	0.81377	0.71
IL1-4/WTpooled	1.03019	1
WT/WTpooled	0.82979	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	0.66888	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99315	1
DC3000/delta hrp 6h	0.94872	0.95
DC3000/delta hrp 12h	0.96006	1
DC3000/delta hrp 24h	0.55079	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51905	0.065
DC3000 delta B/DC3000 delta AB	0.66022	0.067

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85204	1
Exp 36h	0.63645	0.504
Exp 60h	0.36885	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9852	1
Var 0h	1.02441	1
Var 12h I row2-row1	0.69612	0.344
Var 12h NI row2-row1	0.94356	0.82
Var 36h I row2-row1	1.1593	0.601
Var 36h NI row2-row1	1.35373	1
Var 60h I row2-row1	1.0626	1
Var 60h NI row2-row1	0.88723	0.818
Time course 0hI-0hNI	0.93532	0.501
Time course 12hI-12hNI	0.93083	0.42
Time course 36hI-36hNI	0.82354	0.023
Time course 60hI-60hNI	0.1597	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)	1.32512	0.272
transgenic ySAMdc/azygous control (breaker)	1.73873	0.172
transgenic ySAMdc/azygous control (red)	3.02019	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93366	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.02294	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.36442	0.087
Manapal/WT (break)	5.25889	0.183
Manapal/WT (red)	6.84161	0.134