Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.52491	0.029
27DAP/17DAP	1.22378	0.845
39DAP/27DAP	1.0903	0.858
41DAP/39DAP	0.75051	0.189
42DAP/41DAP	2.1087	0.039
43DAP/42DAP	0.74833	0.665
47DAP/43DAP	1.29957	0.415
52DAP/47DAP	1.22191	0.937
57DAP/52DAP	1.46414	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79486	0.03
17DAP/reference	1.2763	0.014
27DAP/reference	1.20361	0.143
39DAP/reference	1.56139	0.018
41DAP/reference	1.40629	0.015
42DAP/reference	1.16595	0.324
43DAP/reference	1.22947	0.013
47DAP/reference	1.33295	0.01
52DAP/reference	1.2995	0.158
57DAP/reference	0.88186	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.83302	0.109
27DAP/17DAP	1.1656	0.506
39DAP/27DAP	1.09054	0.565
41DAP/39DAP	1.13143	1
42DAP/41DAP	1.06639	0.893
43DAP/42DAP	1.33927	0.022
47DAP/43DAP	0.78327	0.028
52DAP/47DAP	1.14171	0.568
57DAP/52DAP	0.95424	0.691
57DAP/7DAP	1.3906	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85409	0.168
17DAP/reference	1.27928	0.049
27DAP/reference	1.21279	0.035
39DAP/reference	1.80242	0.006
41DAP/reference	1.12292	0.199
42DAP/reference	1.30669	0.405
43DAP/reference	1.27031	0.273
47DAP/reference	1.2752	0.068
52DAP/reference	0.95681	0.332
57DAP/reference	0.7872	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88324	0.257
17DAP/reference	1.45983	0.02
27DAP/reference	1.08666	0.316
39DAP/reference	1.20108	0.075
41DAP/reference	0.7292	0.038
42DAP/reference	0.94283	0.392
43DAP/reference	0.92191	0.394
47DAP/reference	1.0264	1
52DAP/reference	0.97227	0.469
57DAP/reference	1.16025	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73413	0.061
17DAP/reference	1.04766	0.706
27DAP/reference	1.3567	0.017
39DAP/reference	1.32167	0.012
41DAP/reference	1.32884	0.02
42DAP/reference	1.50278	0.013
43DAP/reference	1.1693	0.233
47DAP/reference	1.1082	0.239
52DAP/reference	1.23566	0.42
57DAP/reference	1.05446	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.41127	0.85
26DAP/20DAP	0.74593	0.317
34DAP/26DAP	1.46619	0.542
51DAP/34DAP	1.11922	0.98
52DAP/51DAP	0.60991	1
53DAP/52DAP	1.30919	0.37
55DAP/53DAP	1.09201	1
57DAP/55DAP	1.14162	0.881
62DAP/57DAP	1.14013	0.868
68DAP/62DAP	0.98214	0.747
68DAP/14DAP	0.71762	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.79097	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62713	0.188
Mature Green Tomato/Ripe Tomato	2.05767	0.032
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.42559	0.224
Mature Eggplant/Ripe Tomato	0.08224	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19744	0.877
1-1-2/M82	1.55224	1
12-2/M82	1.0482	0.955
12-4/M82	1.05591	1
1-3/M82	0.83243	0.378
2-1-1/M82	1.12796	0.689
2-1/M82	0.76456	0.345
2-6/M82	0.54866	1
3-2/M82	1.86357	0.463
4-1-1/M82	1.69238	0.968
4-1/M82	3.51918	0.853
4-3-2/M82	1.02121	1
4-3/M82	1.12615	1
5-3/M82	0.71839	1
6-2/M82	0.51189	0.481
6-3/M82	7.30903	0.971
7-1/M82	1.47638
7-2/M82	0.63008	0.527
9-3-2/M82	0.78995

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	0.78223	1
IL12-4/WTpooled	1.12912	0.392
IL1-4/WTpooled	0.97111
WT/WTpooled	0.84042	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	0.99777	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03916	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.36435	1
DC3000/delta hrp 24h	1.14033	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07819
Var 0h	0.4799	1
Var 12h I row2-row1	1.33447	0.506
Var 12h NI row2-row1	1.3764	0.649
Var 36h I row2-row1	1.00714	1
Var 36h NI row2-row1	1.23936	0.253
Var 60h I row2-row1	0.97407	0.952
Var 60h NI row2-row1	0.9025	0.818
Time course 0hI-0hNI	1.173	0.323
Time course 12hI-12hNI	1.07906	0.467
Time course 36hI-36hNI	0.85707	0.134
Time course 60hI-60hNI	0.9154	0.319

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)	1.02653	0.921
transgenic ySAMdc/azygous control (breaker)	0.71689	0.142
transgenic ySAMdc/azygous control (red)	0.87589	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09005	0.037

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86117	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91544	1
Manapal/WT (break)	0.31495	0.299
Manapal/WT (red)	2.17818	0.126