Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04224	0.938
27DAP/17DAP	1.41493	0.625
39DAP/27DAP	0.88128	0.537
41DAP/39DAP	0.96636	0.807
42DAP/41DAP	1.21325	0.978
43DAP/42DAP	1.09815	0.985
47DAP/43DAP	1.20557	0.965
52DAP/47DAP	1.17276	0.965
57DAP/52DAP	0.96347	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99777	0.727
17DAP/reference	1.07317	0.166
27DAP/reference	0.94564	0.208
39DAP/reference	1.01572	0.786
41DAP/reference	1.04266	0.451
42DAP/reference	0.87745	0.014
43DAP/reference	1.00692	0.942
47DAP/reference	0.85863	0.011
52DAP/reference	0.72296	0.016
57DAP/reference	0.93484	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84731	0.194
27DAP/17DAP	0.94792	0.878
39DAP/27DAP	1.09007	0.587
41DAP/39DAP	1.09613	0.773
42DAP/41DAP	1.00042	0.894
43DAP/42DAP	0.90826	0.293
47DAP/43DAP	1.02966	0.997
52DAP/47DAP	1.06259	0.868
57DAP/52DAP	0.90747	0.537
57DAP/7DAP	0.92035	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13822	0.274
17DAP/reference	1.19982	0.147
27DAP/reference	1.06152	0.804
39DAP/reference	0.92347	0.198
41DAP/reference	0.93621	0.271
42DAP/reference	1.03827	0.675
43DAP/reference	0.87984	0.1
47DAP/reference	0.80855	0.044
52DAP/reference	0.88858	0.15
57DAP/reference	1.02576	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07281	0.258
17DAP/reference	1.00636	0.873
27DAP/reference	1.04193	1
39DAP/reference	0.82441	0.033
41DAP/reference	0.84038	0.057
42DAP/reference	0.74922	0.012
43DAP/reference	0.9313	0.285
47DAP/reference	0.8576	0.025
52DAP/reference	0.88347	0.006
57DAP/reference	1.06352	0.477

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04238	0.456
17DAP/reference	0.95516	0.55
27DAP/reference	1.05371	0.325
39DAP/reference	0.92431	0.058
41DAP/reference	0.91338	0.293
42DAP/reference	0.8342	0.134
43DAP/reference	0.81548	0.106
47DAP/reference	0.85244	0.049
52DAP/reference	0.95629	0.637
57DAP/reference	0.691	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42454	0.966
26DAP/20DAP	1.06817	0.875
34DAP/26DAP	0.87194	0.771
51DAP/34DAP	0.99972	0.924
52DAP/51DAP	0.95193	1
53DAP/52DAP	1.40516	0.58
55DAP/53DAP	1.1328	0.737
57DAP/55DAP	0.86579	0.658
62DAP/57DAP	1.05063	1
68DAP/62DAP	0.89677	0.579
68DAP/14DAP	0.9312	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30146	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.05092
Immature Eggplant/Mature Eggplant	1.95562	0.165
Ripe Pepper/Ripe Tomato	0.39471
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	N/A	N/A
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	N/A	N/A
5-3/M82	1.10183	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	0.91547
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.35093	0.277
IL2-6/WTpooled	1.07399	0.531
IL7-5/WTpooled	0.37302
IL7-3/WTpooled	0.78955	0.418
IL12-4/WTpooled	0.94865	0.71
IL1-4/WTpooled	0.98929	1
WT/WTpooled	1.01167	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	0.8969	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00153	1
DC3000/delta hrp 6h	0.91663	0.95
DC3000/delta hrp 12h	0.89193	1
DC3000/delta hrp 24h	0.35496	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.21055	0.023
DC3000 delta B/DC3000 delta AB	0.22185	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85994	0.328
Exp 36h	0.63186	0.406
Exp 60h	0.53562	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04979	1
Var 0h	0.57189	0.936
Var 12h I row2-row1	0.98762	1
Var 12h NI row2-row1	0.54071	0.349
Var 36h I row2-row1	0.84956	0.805
Var 36h NI row2-row1	2.03228	1
Var 60h I row2-row1	1.37114	0.543
Var 60h NI row2-row1	1.48464	0.904
Time course 0hI-0hNI	0.73907	0.075
Time course 12hI-12hNI	1.15952	0.237
Time course 36hI-36hNI	1.08523	0.147
Time course 60hI-60hNI	0.06305	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)	1.15703	0.292
transgenic ySAMdc/azygous control (breaker)	0.93914	1
transgenic ySAMdc/azygous control (red)	1.09335	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91818	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.16475	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32274	0.307
Manapal/WT (break)	1.08001	1
Manapal/WT (red)	0.75029	0.181