Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89626	0.532
27DAP/17DAP	0.93378	0.934
39DAP/27DAP	1.02501	0.876
41DAP/39DAP	0.93143	0.717
42DAP/41DAP	0.96571	1
43DAP/42DAP	1.07396	1
47DAP/43DAP	0.8982	0.645
52DAP/47DAP	0.98611	0.752
57DAP/52DAP	0.93051	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83461	0.047
17DAP/reference	0.92043	0.26
27DAP/reference	0.93278	0.417
39DAP/reference	0.9567	0.261
41DAP/reference	1.04756	0.855
42DAP/reference	0.73349	0.129
43DAP/reference	0.97691	0.691
47DAP/reference	0.87379	0.242
52DAP/reference	0.98926	0.618
57DAP/reference	1.02219	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3568	0.247
27DAP/17DAP	0.915	0.854
39DAP/27DAP	1.14651	0.643
41DAP/39DAP	0.99164	0.973
42DAP/41DAP	0.76187	0.052
43DAP/42DAP	0.92644	0.774
47DAP/43DAP	0.78072	0.192
52DAP/47DAP	1.00564	0.935
57DAP/52DAP	0.9419	0.756
57DAP/7DAP	1.18952	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90082	0.1
17DAP/reference	0.8713	0.021
27DAP/reference	0.94811	0.264
39DAP/reference	0.97128	0.474
41DAP/reference	1.03672	0.767
42DAP/reference	1.07857	0.308
43DAP/reference	1.0788	0.432
47DAP/reference	0.91912	0.383
52DAP/reference	1.03511	0.802
57DAP/reference	0.85081	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00896	0.951
17DAP/reference	0.96092	0.474
27DAP/reference	1.03715	0.875
39DAP/reference	1.04929	0.891
41DAP/reference	0.92463	0.194
42DAP/reference	0.98829	0.534
43DAP/reference	1.17044	0.386
47DAP/reference	1.06821	0.353
52DAP/reference	1.00747	1
57DAP/reference	0.85321	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84357	0.082
17DAP/reference	1.05416	0.833
27DAP/reference	0.81588	0.029
39DAP/reference	0.85816	0.083
41DAP/reference	0.97977	0.618
42DAP/reference	1.24274	0.059
43DAP/reference	1.14418	0.168
47DAP/reference	1.02193	0.754
52DAP/reference	0.99937	0.854
57DAP/reference	0.95734	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99328	1
26DAP/20DAP	0.6588	0.317
34DAP/26DAP	2.42902
51DAP/34DAP	0.7317	0.563
52DAP/51DAP	0.86384	1
53DAP/52DAP	1.15844	0.723
55DAP/53DAP	0.49371	0.176
57DAP/55DAP	1.06774	1
62DAP/57DAP	0.76444	0.162
68DAP/62DAP	1.83973	0.336
68DAP/14DAP	1.32969	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79758	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	1.04177
1-3/M82	0.60764
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	0.8121	1
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	N/A	N/A
5-3/M82	0.94151	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.70482	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94053	0.321
IL2-6/WTpooled	0.89608	1
IL7-5/WTpooled	1.22368	0.792
IL7-3/WTpooled	1.05796	1
IL12-4/WTpooled	0.90758	1
IL1-4/WTpooled	1.1184	1
WT/WTpooled	0.92114	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	1.32172	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12406	0.75
DC3000/delta hrp 6h	1.93801
DC3000/delta hrp 12h	0.99273	1
DC3000/delta hrp 24h	0.88548	0.241

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	2.46418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88013	1
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	1.01112	1
Var 0h	0.98434	1
Var 12h I row2-row1	0.91112	0.627
Var 12h NI row2-row1	1.05683	1
Var 36h I row2-row1	0.7384	1
Var 36h NI row2-row1	0.98981	0.852
Var 60h I row2-row1	0.64597	0.285
Var 60h NI row2-row1	0.92753	0.483
Time course 0hI-0hNI	0.99558	1
Time course 12hI-12hNI	1.02352	0.747
Time course 36hI-36hNI	1.19396	0.08
Time course 60hI-60hNI	3.50306	0.008

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)	1.1069	0.863
transgenic ySAMdc/azygous control (breaker)	1.6221	0.248
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96767	0.201

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.50922	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.54711	0.09
Manapal/WT (break)	1.40148	0.14
Manapal/WT (red)	1.42265	0.413