Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88816	0.532
27DAP/17DAP	1.55145	0.552
39DAP/27DAP	1.36915	0.675
41DAP/39DAP	1.25076	0.372
42DAP/41DAP	1.43335	0.844
43DAP/42DAP	0.93202	0.867
47DAP/43DAP	0.86592	0.599
52DAP/47DAP	2.83423	0.538
57DAP/52DAP	0.88402	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	0.91048
27DAP/reference	0.93551
39DAP/reference	1.82303	0.013
41DAP/reference	N/A	N/A
42DAP/reference	0.66776	0.001
43DAP/reference	1.46737
47DAP/reference	0.8183	0.042
52DAP/reference	N/A	N/A
57DAP/reference	0.73718

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39661	0.99
27DAP/17DAP	1.35269	0.912
39DAP/27DAP	1.13553	0.964
41DAP/39DAP	1.72456	0.55
42DAP/41DAP	0.96899	0.797
43DAP/42DAP	1.2215	0.746
47DAP/43DAP	1.00996	0.902
52DAP/47DAP	1.24065	0.635
57DAP/52DAP	1.10949	0.862
57DAP/7DAP	0.86828

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14563	0.223
17DAP/reference	0.96216	0.518
27DAP/reference	0.91708	0.215
39DAP/reference	0.60533	0.013
41DAP/reference	0.64429	0.023
42DAP/reference	0.7036	0.019
43DAP/reference	0.90874	0.183
47DAP/reference	0.94317	0.504
52DAP/reference	0.81912	0.126
57DAP/reference	0.8678	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68755	0.011
17DAP/reference	0.86146	0.113
27DAP/reference	0.87286	0.104
39DAP/reference	0.76737	0.083
41DAP/reference	1.21703	0.766
42DAP/reference	0.82768	0.108
43DAP/reference	0.65033	0.024
47DAP/reference	0.82052	0.044
52DAP/reference	0.89816	0.143
57DAP/reference	0.90152	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94186	0.044
17DAP/reference	0.93791	0.417
27DAP/reference	1.01867	0.672
39DAP/reference	1.02682	0.912
41DAP/reference	1.03192	0.939
42DAP/reference	0.91404	0.172
43DAP/reference	1.09652	0.362
47DAP/reference	1.1665	0.877
52DAP/reference	1.14111	0.443
57DAP/reference	1.42028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10748	1
26DAP/20DAP	0.98728	1
34DAP/26DAP	1.03984	0.988
51DAP/34DAP	1.52132	0.137
52DAP/51DAP	1.29175	0.77
53DAP/52DAP	0.76333	0.051
55DAP/53DAP	1.16117	0.982
57DAP/55DAP	0.74539	0.113
62DAP/57DAP	0.9959	0.994
68DAP/62DAP	1.63961	0.345
68DAP/14DAP	2.61377	0.034

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96881	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.56582
Mature Green Tomato/Ripe Tomato	0.9586	0.715
Immature Eggplant/Mature Eggplant	0.44671
Ripe Pepper/Ripe Tomato	2.22847	1
Mature Eggplant/Ripe Tomato	1.62618

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.85107	0.619
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.12047	1
5-3/M82	1.018	1
6-2/M82	N/A	N/A
6-3/M82	0.7965
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05846	1
IL2-6/WTpooled	0.94315	1
IL7-5/WTpooled	1.51363
IL7-3/WTpooled	0.95544	1
IL12-4/WTpooled	1.52049	0.531
IL1-4/WTpooled	0.95791	1
WT/WTpooled	0.8696	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	1.33605	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.49344	0.846
DC3000/delta hrp 6h	0.92123
DC3000/delta hrp 12h	0.99697	1
DC3000/delta hrp 24h	1.31896	0.422

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	1.37755	0.206

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90645	1
Exp 36h	2.13605	0.693
Exp 60h	1.56468	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93341	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.17248	0.272
Var 12h NI row2-row1	0.89328	0.33
Var 36h I row2-row1	0.81209	0.805
Var 36h NI row2-row1	0.91783	0.791
Var 60h I row2-row1	0.75117	0.285
Var 60h NI row2-row1	1.32721	1
Time course 0hI-0hNI	1.03083	1
Time course 12hI-12hNI	4.50083	0.164
Time course 36hI-36hNI	3.39485	0.004
Time course 60hI-60hNI	5.65381	0.012

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)	0.81492	0.227
transgenic ySAMdc/azygous control (breaker)	0.83669	0.173
transgenic ySAMdc/azygous control (red)	0.97591	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95997	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09658	0.307
Manapal/WT (break)	0.93782	0.299
Manapal/WT (red)	0.90414	0.424