Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95653	0.728
27DAP/17DAP	0.91911	0.814
39DAP/27DAP	1.02162	0.876
41DAP/39DAP	0.80451	0.343
42DAP/41DAP	1.09293	0.92
43DAP/42DAP	1.25029	0.809
47DAP/43DAP	1.47141	0.196
52DAP/47DAP	1.01103	0.837
57DAP/52DAP	1.14266	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07861	0.241
17DAP/reference	0.95983	0.298
27DAP/reference	0.91315	0.194
39DAP/reference	0.96198	0.391
41DAP/reference	0.99453	1
42DAP/reference	0.93261	0.035
43DAP/reference	0.96362	0.555
47DAP/reference	1.01921	1
52DAP/reference	0.98854	0.564
57DAP/reference	0.86805	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12067	0.774
27DAP/17DAP	1.15996	0.311
39DAP/27DAP	1.0439	0.636
41DAP/39DAP	0.89097	0.645
42DAP/41DAP	1.16419	0.049
43DAP/42DAP	0.83718	0.06
47DAP/43DAP	0.97802	0.902
52DAP/47DAP	1.68095	0.066
57DAP/52DAP	0.99337	0.848
57DAP/7DAP	1.29383	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07035	0.444
17DAP/reference	1.076	0.971
27DAP/reference	0.87703	0.066
39DAP/reference	0.97659	0.474
41DAP/reference	0.90584	0.247
42DAP/reference	0.84458	0.13
43DAP/reference	0.88897	0.069
47DAP/reference	1.01654	1
52DAP/reference	0.80002	0.046
57DAP/reference	1.10714	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03565	0.732
17DAP/reference	0.99629	0.786
27DAP/reference	0.96169	0.393
39DAP/reference	0.9342	0.165
41DAP/reference	0.83637	0.031
42DAP/reference	0.87054	0.039
43DAP/reference	0.98107	0.657
47DAP/reference	0.87627	0.025
52DAP/reference	0.99667	0.713
57DAP/reference	1.0507	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03974	1
17DAP/reference	0.97478	0.579
27DAP/reference	0.94814	0.337
39DAP/reference	0.9832	0.643
41DAP/reference	0.93781	0.371
42DAP/reference	0.96053	0.552
43DAP/reference	0.89944	0.131
47DAP/reference	0.96225	0.315
52DAP/reference	1.07095	0.941
57DAP/reference	0.92996	0.199

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94987	1
26DAP/20DAP	0.85418	1
34DAP/26DAP	1.42597	0.819
51DAP/34DAP	0.91082	0.77
52DAP/51DAP	1.15268	0.542
53DAP/52DAP	1.38782	0.398
55DAP/53DAP	0.97882	0.82
57DAP/55DAP	0.90564	0.548
62DAP/57DAP	1.09088	0.515
68DAP/62DAP	1.16841	0.616
68DAP/14DAP	1.05565	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.99663	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84711	0.309
Mature Green Tomato/Ripe Tomato	0.79492	0.317
Immature Eggplant/Mature Eggplant	0.87476	0.144
Ripe Pepper/Ripe Tomato	1.20818	1
Mature Eggplant/Ripe Tomato	1.26672	1

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	0.80302	0.274
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	1.38231
4-3/M82	1.01639
5-3/M82	1.07204
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.88932	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17619
IL2-6/WTpooled	0.50728
IL7-5/WTpooled	1.00417	1
IL7-3/WTpooled	1.15022	1
IL12-4/WTpooled	1.08663	0.737
IL1-4/WTpooled	1.04305	1
WT/WTpooled	0.98149	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	1.08691	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13635	0.656
DC3000/delta hrp 6h	1.0956	1
DC3000/delta hrp 12h	0.90398	1
DC3000/delta hrp 24h	3.37553	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.58266
DC3000 delta B/DC3000 delta AB	0.4843	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77349	0.328
Exp 36h	0.82817	0.406
Exp 60h	0.82154	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00689	1
Var 0h	0.86074	1
Var 12h I row2-row1	0.82585	0.338
Var 12h NI row2-row1	0.86929	0.443
Var 36h I row2-row1	0.67019	1
Var 36h NI row2-row1	1.67118	1
Var 60h I row2-row1	1.05147	1
Var 60h NI row2-row1	1.01372	1
Time course 0hI-0hNI	1.03132	0.867
Time course 12hI-12hNI	0.94176	0.632
Time course 36hI-36hNI	0.7946	0.03
Time course 60hI-60hNI	0.27748	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)	0.9824	0.409
transgenic ySAMdc/azygous control (breaker)	1.28743	0.178
transgenic ySAMdc/azygous control (red)	1.19196	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9803	0.263

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.67954	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.67155	0.084
Manapal/WT (break)	1.06297	1
Manapal/WT (red)	0.83394	0.424