PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0016874
Description: ligase activity

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_7	6	CH_aly_33	10	25	0.000000151296
Arabidopsis thaliana	1	1	CH_ath_292	12	80	0.00032513
Arabidopsis thaliana	1	2	CH_ath_371	12	80	0.00036537
Arabidopsis thaliana	1	3	CH_ath_435	12	80	0.000642013
Arabidopsis thaliana	1	4	CH_ath_72	14	98	0.0000369065
Arabidopsis thaliana	1	5	CH_ath_89	14	98	0.0000422601
Arabidopsis thaliana	1	6	CH_ath_107	14	98	0.0000812908
Oryza sativa ssp. japonica	5	5	CH_osa_167	11	132	0.00054577
Oryza sativa ssp. japonica	1	9	CH_osa_35	8	48	0.000140788
Theobroma cacao	scaffold_9	1	CH_tca_245	4	4	0.000190924
Theobroma cacao	scaffold_9	2	CH_tca_364	4	4	0.000770739

Available child term results

GO term	Description	Number of clusters
GO:0003883	CTP synthase activity	6
GO:0003910	DNA ligase (ATP) activity	18
GO:0003952	NAD+ synthase (glutamine-hydrolyzing) activity	7
GO:0003972	RNA ligase (ATP) activity	4
GO:0004019	adenylosuccinate synthase activity	2
GO:0004055	argininosuccinate synthase activity	17
GO:0004075	biotin carboxylase activity	18
GO:0004326	tetrahydrofolylpolyglutamate synthase activity	6
GO:0004329	formate-tetrahydrofolate ligase activity	6
GO:0004356	glutamate-ammonia ligase activity	8
GO:0004357	glutamate-cysteine ligase activity	7
GO:0004363	glutathione synthase activity	16
GO:0004632	phosphopantothenate--cysteine ligase activity	1
GO:0004637	phosphoribosylamine-glycine ligase activity	14
GO:0004639	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity	3
GO:0004642	phosphoribosylformylglycinamidine synthase activity	1
GO:0004775	succinate-CoA ligase (ADP-forming) activity	10
GO:0004817	cysteine-tRNA ligase activity	4
GO:0004820	glycine-tRNA ligase activity	1
GO:0004821	histidine-tRNA ligase activity	3
GO:0004822	isoleucine-tRNA ligase activity	5
GO:0004823	leucine-tRNA ligase activity	1
GO:0004824	lysine-tRNA ligase activity	6
GO:0004826	phenylalanine-tRNA ligase activity	1
GO:0004827	proline-tRNA ligase activity	1
GO:0004828	serine-tRNA ligase activity	1
GO:0004829	threonine-tRNA ligase activity	1
GO:0004832	valine-tRNA ligase activity	2
GO:0004842	ubiquitin-protein ligase activity	15
GO:0008716	D-alanine-D-alanine ligase activity	6
GO:0008841	dihydrofolate synthase activity	2
GO:0008922	long-chain fatty acid [acyl-carrier-protein] ligase activity	7
GO:0010279	indole-3-acetic acid amido synthetase activity	3
GO:0016207	4-coumarate-CoA ligase activity	11
GO:0016405	CoA-ligase activity	4
GO:0016851	magnesium chelatase activity	3
GO:0016877	ligase activity, forming carbon-sulfur bonds	3
GO:0016879	ligase activity, forming carbon-nitrogen bonds	3
GO:0016881	acid-amino acid ligase activity	17
GO:0016884	carbon-nitrogen ligase activity, with glutamine as amido-N-donor	57
GO:0016992	lipoate synthase activity	24
GO:0018858	benzoate-CoA ligase activity	11
GO:0030272	5-formyltetrahydrofolate cyclo-ligase activity	3
GO:0031957	very long-chain fatty acid-CoA ligase activity	8
GO:0034450	ubiquitin-ubiquitin ligase activity	3
GO:0080123	jasmonate-amino synthetase activity	3

Functional clusters experiments

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