Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.8.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87957	0.522
27DAP/17DAP	1.10352	0.849
39DAP/27DAP	1.13346	0.638
41DAP/39DAP	0.74545	0.156
42DAP/41DAP	0.99682	1
43DAP/42DAP	1.15445	0.954
47DAP/43DAP	0.66706	0.133
52DAP/47DAP	1.11203	0.934
57DAP/52DAP	1.17096	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1305	0.48
17DAP/reference	0.88536	0.043
27DAP/reference	0.95676	0.538
39DAP/reference	0.85058	0.149
41DAP/reference	0.92471	0.267
42DAP/reference	1.13348	0.019
43DAP/reference	0.92668	0.234
47DAP/reference	0.92031	0.077
52DAP/reference	0.94763	0.382
57DAP/reference	0.93659	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22444	0.094
27DAP/17DAP	0.96435	0.748
39DAP/27DAP	0.67506	0.029
41DAP/39DAP	1.1017	0.817
42DAP/41DAP	0.8652	0.199
43DAP/42DAP	0.85122	0.034
47DAP/43DAP	0.89728	0.447
52DAP/47DAP	0.98695	0.93
57DAP/52DAP	1.32164	0.047
57DAP/7DAP	0.96277	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0172	1
17DAP/reference	1.02161	1
27DAP/reference	1.21726	0.088
39DAP/reference	0.69518	0.012
41DAP/reference	0.91528	0.311
42DAP/reference	1.04728	0.791
43DAP/reference	0.96118	0.459
47DAP/reference	1.03864	0.98
52DAP/reference	1.28938	0.092
57DAP/reference	1.14565	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95647	0.639
17DAP/reference	1.22594	0.181
27DAP/reference	1.23839	0.052
39DAP/reference	1.4573	0.018
41DAP/reference	1.4191	0.007
42DAP/reference	1.47818	0.007
43DAP/reference	0.93605	0.385
47DAP/reference	1.00236	0.678
52DAP/reference	1.44599	0.006
57DAP/reference	0.86119	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9003	0.135
17DAP/reference	0.96907	0.647
27DAP/reference	1.16667	0.207
39DAP/reference	1.03833	0.858
41DAP/reference	0.86253	0.331
42DAP/reference	1.09243	0.408
43DAP/reference	1.01916	0.961
47DAP/reference	0.7336	0.016
52DAP/reference	1.01024	0.871
57DAP/reference	0.96121	0.475

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.83748	0.786
26DAP/20DAP	1.09805	1
34DAP/26DAP	0.91034	0.803
51DAP/34DAP	0.86101	0.66
52DAP/51DAP	0.88022	1
53DAP/52DAP	0.93382	0.715
55DAP/53DAP	1.51218	0.487
57DAP/55DAP	0.94043	0.718
62DAP/57DAP	0.95528	0.994
68DAP/62DAP	1.05951	0.926
68DAP/14DAP	0.86833	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.57665	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84265	0.304
Mature Green Tomato/Ripe Tomato	1.57699	0.025
Immature Eggplant/Mature Eggplant	0.78962	0.096
Ripe Pepper/Ripe Tomato	2.7104	1
Mature Eggplant/Ripe Tomato	1.38912	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.04961	1
12-2/M82	N/A	N/A
12-4/M82	0.98395	1
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.49309
4-3-2/M82	1.33146	0.508
4-3/M82	N/A	N/A
5-3/M82	0.85249	0.334
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.82386
9-3-2/M82	1.30856	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31534	0.493
IL2-6/WTpooled	0.83912	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.28017	1
IL12-4/WTpooled	1.32163	0.532
IL1-4/WTpooled	0.86454	0.444
WT/WTpooled	1.00041	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	1.05721	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08252	0.921
DC3000/delta hrp 6h	0.90717	0.95
DC3000/delta hrp 12h	0.93255	1
DC3000/delta hrp 24h	1.00989	0.957

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56458	0.023
DC3000 delta B/DC3000 delta AB	0.76269	0.058

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89757	1
Exp 36h	0.79796	0.456
Exp 60h	0.68293	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99679	1
Var 0h	4.94684	0.936
Var 12h I row2-row1	0.74085	0.338
Var 12h NI row2-row1	0.86169	0.546
Var 36h I row2-row1	0.88293	0.575
Var 36h NI row2-row1	1.21391	1
Var 60h I row2-row1	1.12758	1
Var 60h NI row2-row1	0.95873	1
Time course 0hI-0hNI	0.9696	0.835
Time course 12hI-12hNI	0.94135	0.47
Time course 36hI-36hNI	0.81964	0.023
Time course 60hI-60hNI	0.10572	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)	1.25233	0.3
transgenic ySAMdc/azygous control (breaker)	0.80561	0.139
transgenic ySAMdc/azygous control (red)	0.97523	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93963	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68572	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07441	1
Manapal/WT (break)	0.78539	1
Manapal/WT (red)	1.80684	0.164