Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88798	0.413
27DAP/17DAP	0.91162	0.807
39DAP/27DAP	1.01613	0.899
41DAP/39DAP	1.2374	0.814
42DAP/41DAP	1.20088	0.863
43DAP/42DAP	0.97148	0.912
47DAP/43DAP	0.91192	0.667
52DAP/47DAP	1.13336	0.786
57DAP/52DAP	1.0465	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03447	0.685
17DAP/reference	0.99237	0.819
27DAP/reference	0.97378	0.525
39DAP/reference	0.96487	0.527
41DAP/reference	0.94154	0.267
42DAP/reference	0.88812	0.002
43DAP/reference	0.97322	0.594
47DAP/reference	1.01164	1
52DAP/reference	0.78171	0.017
57DAP/reference	1.35286	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8198	0.065
27DAP/17DAP	0.91123	0.475
39DAP/27DAP	1.00632	1
41DAP/39DAP	0.95175	0.839
42DAP/41DAP	1.03288	0.904
43DAP/42DAP	1.21677	0.273
47DAP/43DAP	0.97363	0.877
52DAP/47DAP	0.917	0.634
57DAP/52DAP	0.85642	0.113
57DAP/7DAP	0.75537	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06796	0.564
17DAP/reference	0.96981	0.108
27DAP/reference	0.961	0.248
39DAP/reference	0.88284	0.013
41DAP/reference	0.9484	0.284
42DAP/reference	0.90031	0.027
43DAP/reference	0.90399	0.145
47DAP/reference	0.923	0.293
52DAP/reference	1.00362	1
57DAP/reference	0.87764	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93456	0.457
17DAP/reference	0.94918	0.399
27DAP/reference	0.938	0.34
39DAP/reference	0.90443	0.071
41DAP/reference	0.98169	0.481
42DAP/reference	0.92719	0.108
43DAP/reference	0.78159	0.018
47DAP/reference	0.89953	0.01
52DAP/reference	0.80958	0.007
57DAP/reference	0.81643	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94633	0.311
17DAP/reference	1.11692	0.269
27DAP/reference	1.05072	0.171
39DAP/reference	1.00256	1
41DAP/reference	0.95236	0.371
42DAP/reference	0.84536	0.023
43DAP/reference	0.87018	0.048
47DAP/reference	0.85323	0.012
52DAP/reference	0.99615	0.871
57DAP/reference	1.76846	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03678	0.966
26DAP/20DAP	1.10696	0.762
34DAP/26DAP	0.90824	0.816
51DAP/34DAP	1.11097	0.909
52DAP/51DAP	0.88275	1
53DAP/52DAP	1.24015	0.58
55DAP/53DAP	1.13701	0.703
57DAP/55DAP	1.07951	0.854
62DAP/57DAP	1.32172	0.678
68DAP/62DAP	0.95923	0.787
68DAP/14DAP	0.88285	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.11529	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.06592	0.058
Mature Green Tomato/Ripe Tomato	1.01031	0.774
Immature Eggplant/Mature Eggplant	0.54918	0.062
Ripe Pepper/Ripe Tomato	3.79088	1
Mature Eggplant/Ripe Tomato	42.397	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18233
1-1-2/M82	1.70696
12-2/M82	N/A	N/A
12-4/M82	1.61199
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	0.81113
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	2.26813
4-3/M82	N/A	N/A
5-3/M82	1.13811	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.64357
9-3-2/M82	1.8103

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.48188
IL2-6/WTpooled	1.00024	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02198	1
IL12-4/WTpooled	1.03789	0.891
IL1-4/WTpooled	1.10071	1
WT/WTpooled	0.98135	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	0.72838	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89166	0.941
DC3000/delta hrp 6h	0.99696	0.95
DC3000/delta hrp 12h	0.94688	1
DC3000/delta hrp 24h	0.82373	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55576	0.033
DC3000 delta B/DC3000 delta AB	0.65278	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94942	1
Exp 36h	0.85089	0.434
Exp 60h	0.87955	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01953	1
Var 0h	0.84872	0.933
Var 12h I row2-row1	0.51228	0.338
Var 12h NI row2-row1	1.03893	1
Var 36h I row2-row1	0.74318	0.374
Var 36h NI row2-row1	1.39128	0.482
Var 60h I row2-row1	1.10928	1
Var 60h NI row2-row1	0.98797	1
Time course 0hI-0hNI	1.027	0.833
Time course 12hI-12hNI	0.90579	0.225
Time course 36hI-36hNI	0.82708	0.029
Time course 60hI-60hNI	0.12584	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)	0.97566	0.485
transgenic ySAMdc/azygous control (breaker)	2.66056	0.165
transgenic ySAMdc/azygous control (red)	0.94529	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87357	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28168	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.53541	0.083
Manapal/WT (break)	3.61615	0.126
Manapal/WT (red)	3.76139	0.413