PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00024	3	CH_atr_312	3	3	0.000428787
Amborella trichopoda	scaffold00024	6	CH_atr_64	10	263	0.0000392721
Capsella rubella	scaffold_3	1	CH_cru_165	3	3	0.0000931515
Medicago truncatula	chr1	1	CH_mtr_318	4	8	0.00000360134
Medicago truncatula	chr1	2	CH_mtr_389	4	8	0.00000817615
Medicago truncatula	chr1	3	CH_mtr_528	4	8	0.0000256434
Physcomitrella patens	scaffold_102	1	CH_ppa_38	4	9	0.000117795
Prunus persica	scaffold_4	1	CH_ppe_160	4	5	0.000000512986
Prunus persica	scaffold_4	2	CH_ppe_206	4	5	0.00000164306
Prunus persica	scaffold_4	3	CH_ppe_250	4	5	0.00000238026
Solanum lycopersicum	ch08	1	CH_sly_67	7	8	0.000000000000310294
Solanum lycopersicum	ch08	1	CH_sly_237	4	5	0.0000102119
Solanum tuberosum	chr07	1	CH_stu_432	3	3	0.000222481
Solanum tuberosum	chr08	1	CH_stu_125	6	7	0.00000000000854834
Solanum tuberosum	chr07	2	CH_stu_531	3	3	0.000369875
Solanum tuberosum	chr03	3	CH_stu_758	3	3	0.000739478
Solanum tuberosum	chr07	3	CH_stu_757	3	3	0.000739478
Solanum tuberosum	chr08	3	CH_stu_111	8	10	0.00000000000000430678
Theobroma cacao	scaffold_5	1	CH_tca_216	3	3	0.0000637094
Theobroma cacao	scaffold_5	2	CH_tca_266	3	3	0.000145174
Theobroma cacao	scaffold_5	3	CH_tca_372	3	3	0.000263649
Vitis vinifera	chr4	1	CH_vvi_304	3	5	0.000773836

GO term	Description	Number of clusters
GO:0004058	aromatic-L-amino-acid decarboxylase activity	1
GO:0004163	diphosphomevalonate decarboxylase activity	3
GO:0004351	glutamate decarboxylase activity	31
GO:0004425	indole-3-glycerol-phosphate synthase activity	18
GO:0004586	ornithine decarboxylase activity	3
GO:0004590	orotidine-5'-phosphate decarboxylase activity	2
GO:0004609	phosphatidylserine decarboxylase activity	14
GO:0004612	phosphoenolpyruvate carboxykinase (ATP) activity	7
GO:0004638	phosphoribosylaminoimidazole carboxylase activity	9
GO:0004737	pyruvate decarboxylase activity	3
GO:0004853	uroporphyrinogen decarboxylase activity	11
GO:0008792	arginine decarboxylase activity	1
GO:0008836	diaminopimelate decarboxylase activity	1
GO:0008964	phosphoenolpyruvate carboxylase activity	12
GO:0016984	ribulose-bisphosphate carboxylase activity	25
GO:0047434	indolepyruvate decarboxylase activity	1
GO:0048040	UDP-glucuronate decarboxylase activity	1
GO:0050080	malonyl-CoA decarboxylase activity	6

Exp id	Data type	Data filter	Min genes cluster	Max genes cluster	Max cluster size	E-value	Tandems removal
1	GO	Primary GO data only.	2	30	80	0.001	X
2	GO	Primary and orthology projected GO data.	2	30	80	0.001	X
3	GO	All GO data.	2	30	80	0.001	X
4	GO	Primary GO data only.	10	150	300	0.001	X
5	GO	Primary and orthology projected GO data.	10	150	300	0.001	X
6	GO	All GO data.	10	150	300	0.001	X
7	GO	Primary GO data only.	2	30	80	0.001	V
8	GO	Primary and orthology projected GO data.	2	30	80	0.001	V
9	GO	All GO data.	2	30	80	0.001	V
10	GO	Primary GO data only.	10	150	300	0.001	V
11	GO	Primary and orthology projected GO data.	10	150	300	0.001	V
12	GO	All GO data.	10	150	300	0.001	V
13	InterPro	No filter applied.	2	30	80	0.001	X
14	InterPro	No filter applied.	10	150	300	0.001	X
15	InterPro	No filter applied.	2	30	80	0.001	V
16	InterPro	No filter applied.	10	150	300	0.001	V
17	MapMan	No filter applied.	2	30	80	0.001	X
18	MapMan	No filter applied.	10	150	300	0.001	X
19	MapMan	No filter applied.	2	30	80	0.001	V
20	MapMan	No filter applied.	10	150	300	0.001	V