Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.16.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05609	0.964
27DAP/17DAP	1.0075	1
39DAP/27DAP	1.15876	0.956
41DAP/39DAP	1.102	0.657
42DAP/41DAP	1.03045	1
43DAP/42DAP	1.07299	1
47DAP/43DAP	1.06308	1
52DAP/47DAP	0.76189	0.42
57DAP/52DAP	1.4909	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92207	0.262
17DAP/reference	0.79298	0.009
27DAP/reference	1.00982	0.847
39DAP/reference	0.98339	0.779
41DAP/reference	0.83906	0.114
42DAP/reference	0.89879	0.012
43DAP/reference	0.89545	0.222
47DAP/reference	0.98557	0.503
52DAP/reference	1.04306	0.878
57DAP/reference	1.15603	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97536	0.679
27DAP/17DAP	1.23249	0.632
39DAP/27DAP	1.20902	0.388
41DAP/39DAP	0.94191	0.875
42DAP/41DAP	1.33335	0.478
43DAP/42DAP	0.97619	0.854
47DAP/43DAP	0.98586	0.911
52DAP/47DAP	1.1322	0.785
57DAP/52DAP	1.48534	0.276
57DAP/7DAP	1.1767	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02389	1
17DAP/reference	1.11923	0.328
27DAP/reference	1.09272	0.453
39DAP/reference	0.79874	0.064
41DAP/reference	0.86333	0.094
42DAP/reference	0.92729	0.169
43DAP/reference	0.9332	0.266
47DAP/reference	0.66869	0.101
52DAP/reference	0.77454	0.014
57DAP/reference	0.88124	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93814	0.548
17DAP/reference	1.02544	0.92
27DAP/reference	0.98101	0.554
39DAP/reference	0.99942	0.682
41DAP/reference	0.96439	0.432
42DAP/reference	1.0642	0.664
43DAP/reference	0.96705	0.539
47DAP/reference	0.84008	0.085
52DAP/reference	0.92265	0.259
57DAP/reference	0.96192	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91014	0.23
17DAP/reference	1.00904	0.934
27DAP/reference	1.01334	0.883
39DAP/reference	0.96884	0.504
41DAP/reference	1.03043	1
42DAP/reference	0.9771	0.671
43DAP/reference	1.00125	0.796
47DAP/reference	0.99952	0.646
52DAP/reference	1.14197	0.335
57DAP/reference	1.18303	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33911	0.966
26DAP/20DAP	1.21794	0.567
34DAP/26DAP	1.71144	1
51DAP/34DAP	0.99814	0.967
52DAP/51DAP	0.75848	1
53DAP/52DAP	1.25469	0.608
55DAP/53DAP	0.80932	0.018
57DAP/55DAP	1.21257	0.805
62DAP/57DAP	0.97453	0.994
68DAP/62DAP	0.89192	0.769
68DAP/14DAP	1.29329	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02296	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62353	0.155
Mature Green Tomato/Ripe Tomato	0.94645	0.522
Immature Eggplant/Mature Eggplant	1.1541	0.096
Ripe Pepper/Ripe Tomato	1.56789	1
Mature Eggplant/Ripe Tomato	1.2138	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.628	0.402
1-1-2/M82	0.63291
12-2/M82	1.20544	0.61
12-4/M82	0.65312	0.298
1-3/M82	0.85988
2-1-1/M82	0.82367
2-1/M82	0.67235
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.57319	0.698
4-3/M82	0.76379	0.72
5-3/M82	1.03567	1
6-2/M82	0.68893	1
6-3/M82	1.48252	1
7-1/M82	N/A	N/A
7-2/M82	0.98037
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	14.3569
WT/WTpooled	N/A	N/A

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	0.8846	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92329	0.941
DC3000/delta hrp 6h	0.73914	0.942
DC3000/delta hrp 12h	1.13552	1
DC3000/delta hrp 24h	1.07872	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.16175
DC3000 delta B/DC3000 delta AB	0.51331	0.031

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88452	0.265
Exp 36h	0.72132	0.539
Exp 60h	0.85394	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05059	1
Var 0h	1.27538	0.782
Var 12h I row2-row1	0.89527	0.357
Var 12h NI row2-row1	1.01717	1
Var 36h I row2-row1	1.1276	1
Var 36h NI row2-row1	1.09175	1
Var 60h I row2-row1	0.96469	0.306
Var 60h NI row2-row1	1.11237	0.904
Time course 0hI-0hNI	1.08422	0.833
Time course 12hI-12hNI	0.87806	0.272
Time course 36hI-36hNI	0.77491	0.049
Time course 60hI-60hNI	0.33423	0.006

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)	1.25678	0.268
transgenic ySAMdc/azygous control (breaker)	0.75112	0.173
transgenic ySAMdc/azygous control (red)	0.73913	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11027	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.51723	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01605	1
Manapal/WT (break)	0.86411	0.333
Manapal/WT (red)	0.98732	0.863