Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74128	0.057
27DAP/17DAP	0.92823	0.86
39DAP/27DAP	1.15518	0.725
41DAP/39DAP	0.81337	0.401
42DAP/41DAP	1.08665	0.926
43DAP/42DAP	1.09564	1
47DAP/43DAP	0.83121	0.424
52DAP/47DAP	1.37727	0.407
57DAP/52DAP	1.21013	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.99221	0.011
17DAP/reference	1.25398	0.132
27DAP/reference	0.97108	0.642
39DAP/reference	1.1319	0.044
41DAP/reference	1.14515	0.221
42DAP/reference	1.26001	0.001
43DAP/reference	1.03643	0.705
47DAP/reference	1.19068	0.008
52DAP/reference	1.16627	0.023
57DAP/reference	1.03582	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85453	0.336
27DAP/17DAP	0.85097	0.537
39DAP/27DAP	0.84062	0.334
41DAP/39DAP	1.17935	0.393
42DAP/41DAP	1.01053	0.87
43DAP/42DAP	1.03011	0.83
47DAP/43DAP	1.04454	0.951
52DAP/47DAP	0.99616	0.959
57DAP/52DAP	0.75519	0.494
57DAP/7DAP	1.48209	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.957	0.024
17DAP/reference	1.96331	0.006
27DAP/reference	1.98778	0.007
39DAP/reference	1.06822	0.411
41DAP/reference	1.73909	0.011
42DAP/reference	1.70902	0.013
43DAP/reference	1.8407	0.012
47DAP/reference	1.57847	0.018
52DAP/reference	1.50713	0.121
57DAP/reference	0.87074	0.128

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.78746	0.049
17DAP/reference	1.60895	0.018
27DAP/reference	1.69756	0.013
39DAP/reference	1.32192	0.213
41DAP/reference	1.54262	0.008
42DAP/reference	1.78586	0.007
43DAP/reference	1.18608	0.222
47DAP/reference	1.28543	0.035
52DAP/reference	1.2877	0.046
57DAP/reference	1.17537	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.55961	0.015
17DAP/reference	1.43809	0.166
27DAP/reference	1.86841	0.013
39DAP/reference	1.30065	0.013
41DAP/reference	1.05442	0.777
42DAP/reference	1.14189	0.459
43DAP/reference	1.31057	0.331
47DAP/reference	1.09352	0.901
52DAP/reference	1.01397	0.854
57DAP/reference	1.33065	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.84036	0.915
26DAP/20DAP	0.97044	1
34DAP/26DAP	0.87898	0.682
51DAP/34DAP	1.01099	1
52DAP/51DAP	1.24182	0.054
53DAP/52DAP	1.10941	0.753
55DAP/53DAP	1.65309	0.185
57DAP/55DAP	1.38575	0.559
62DAP/57DAP	0.77102	0.162
68DAP/62DAP	1.24397	0.597
68DAP/14DAP	1.39746	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.70576	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.4588	0.058
Mature Green Tomato/Ripe Tomato	0.89709	0.377
Immature Eggplant/Mature Eggplant	0.84295	0.125
Ripe Pepper/Ripe Tomato	1.24661	1
Mature Eggplant/Ripe Tomato	1.98077	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88223	0.944
1-1-2/M82	1.16771
12-2/M82	1.65079	1
12-4/M82	1.09276	0.611
1-3/M82	2.78673
2-1-1/M82	0.61786
2-1/M82	0.63489
2-6/M82	0.78246
3-2/M82	1.18646
4-1-1/M82	1.18943
4-1/M82	1.23384
4-3-2/M82	1.19313	1
4-3/M82	1.32478	1
5-3/M82	0.96347	1
6-2/M82	3.28061	0.212
6-3/M82	0.94684
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.21921

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.6009	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.51092
IL12-4/WTpooled	1.50893
IL1-4/WTpooled	2.16231	1
WT/WTpooled	1.15424	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	1.04153	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06447	0.921
DC3000/delta hrp 6h	0.9189	0.95
DC3000/delta hrp 12h	1.1592
DC3000/delta hrp 24h	1.77032	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.69193	0.046
DC3000 delta B/DC3000 delta AB	1.09178	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97414	1
Exp 36h	1.06421	1
Exp 60h	0.9396	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94084	1
Var 0h	1.03392	0.936
Var 12h I row2-row1	0.99138	1
Var 12h NI row2-row1	0.91753	0.906
Var 36h I row2-row1	1.36708	0.742
Var 36h NI row2-row1	0.98943	0.852
Var 60h I row2-row1	0.89152	0.582
Var 60h NI row2-row1	0.75765	0.359
Time course 0hI-0hNI	0.89693	0.202
Time course 12hI-12hNI	1.03337	0.803
Time course 36hI-36hNI	1.14323	0.453
Time course 60hI-60hNI	1.13982	0.08

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)	1.13042	0.325
transgenic ySAMdc/azygous control (breaker)	0.74018	0.173
transgenic ySAMdc/azygous control (red)	0.94874	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91036	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77081	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07924	1
Manapal/WT (break)	1.07092	1
Manapal/WT (red)	0.85485	0.424