Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17552	0.827
27DAP/17DAP	1.35927	0.742
39DAP/27DAP	0.89649	0.652
41DAP/39DAP	0.84048	0.419
42DAP/41DAP	0.90086	0.751
43DAP/42DAP	1.15664	0.88
47DAP/43DAP	1.41162	0.668
52DAP/47DAP	0.85453	0.637
57DAP/52DAP	0.8844	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.36718
17DAP/reference	0.74469	0.091
27DAP/reference	0.73573	0.085
39DAP/reference	N/A	N/A
41DAP/reference	N/A	N/A
42DAP/reference	0.91069	0.25
43DAP/reference	0.52141
47DAP/reference	0.78463	0.014
52DAP/reference	0.96459
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37969	0.196
27DAP/17DAP	0.98685	0.943
39DAP/27DAP	0.91214	0.529
41DAP/39DAP	0.87214	0.398
42DAP/41DAP	0.97245	0.751
43DAP/42DAP	1.83618	0.413
47DAP/43DAP	0.92248	0.31
52DAP/47DAP	1.12402	0.603
57DAP/52DAP	1.01388	0.776
57DAP/7DAP	1.16745	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13167	0.444
17DAP/reference	1.2682	0.059
27DAP/reference	1.14213	0.088
39DAP/reference	0.73676	0.17
41DAP/reference	0.80694	0.027
42DAP/reference	0.73641	0.014
43DAP/reference	1.14321	0.537
47DAP/reference	0.99501	0.671
52DAP/reference	1.09438	0.428
57DAP/reference	1.25652	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74156	0.058
17DAP/reference	0.78533	0.099
27DAP/reference	0.9504	0.269
39DAP/reference	0.93291	0.392
41DAP/reference	0.93068	0.364
42DAP/reference	0.95719	0.355
43DAP/reference	1.0609	0.736
47DAP/reference	1.00245	0.812
52DAP/reference	0.79563	0.027
57DAP/reference	0.7285	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05498	0.588
17DAP/reference	0.96248	0.56
27DAP/reference	1.13564	0.149
39DAP/reference	1.03508	0.691
41DAP/reference	0.99916	0.754
42DAP/reference	1.24752	0.037
43DAP/reference	1.40279	0.016
47DAP/reference	0.88541	0.278
52DAP/reference	1.20832	0.335
57DAP/reference	1.24422	0.279

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22928	1
26DAP/20DAP	1.00648	1
34DAP/26DAP	0.98856	0.954
51DAP/34DAP	1.16284	0.627
52DAP/51DAP	0.98718	1
53DAP/52DAP	1.01136	0.97
55DAP/53DAP	0.90563	0.663
57DAP/55DAP	1.00567	0.944
62DAP/57DAP	0.95073	0.871
68DAP/62DAP	2.38414	0.01
68DAP/14DAP	2.44562	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68387	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88942	0.41
Mature Green Tomato/Ripe Tomato	1.05357	0.523
Immature Eggplant/Mature Eggplant	0.73371	0.068
Ripe Pepper/Ripe Tomato	2.05302	0.258
Mature Eggplant/Ripe Tomato	3.76618	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10538	1
1-1-2/M82	1.18287	0.977
12-2/M82	1.01592
12-4/M82	1.00309	1
1-3/M82	0.71755
2-1-1/M82	0.9319	0.92
2-1/M82	0.89715
2-6/M82	0.95639
3-2/M82	1.38043	0.426
4-1-1/M82	N/A	N/A
4-1/M82	2.64526
4-3-2/M82	N/A	N/A
4-3/M82	1.06212	1
5-3/M82	0.89375	0.642
6-2/M82	1.46611
6-3/M82	0.86612	0.433
7-1/M82	0.9213	1
7-2/M82	1.09529	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03482
IL2-6/WTpooled	0.91118	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0946	1
IL12-4/WTpooled	1.04941	0.785
IL1-4/WTpooled	1.04777	1
WT/WTpooled	1.03778	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	0.81209	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91716	1
DC3000/delta hrp 6h	1.00293	0.95
DC3000/delta hrp 12h	0.93191	1
DC3000/delta hrp 24h	1.36958	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06246	1
DC3000 delta B/DC3000 delta AB	1.71759	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78798	1
Exp 36h	0.83169	0.589
Exp 60h	0.84734	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99227	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.96277	0.627
Var 12h NI row2-row1	1.11901	0.281
Var 36h I row2-row1	1.06058	1
Var 36h NI row2-row1	0.87596	0.45
Var 60h I row2-row1	0.97797	0.582
Var 60h NI row2-row1	1.08968	0.904
Time course 0hI-0hNI	0.96983	0.863
Time course 12hI-12hNI	0.98058	0.882
Time course 36hI-36hNI	0.90111	0.102
Time course 60hI-60hNI	0.61368	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)	1.15173	0.384
transgenic ySAMdc/azygous control (breaker)	1.32728	0.172
transgenic ySAMdc/azygous control (red)	1.12913	0.92

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	1.37423	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.43988	0.096
Manapal/WT (break)	0.97664	1
Manapal/WT (red)	0.99036	0.863