PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0006520
Description: cellular amino acid metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Oryza sativa ssp. japonica	10	3	CH_osa_238	7	19	0.0000064029
Populus trichocarpa	Chr03	1	CH_ptr_345	4	4	0.000602789
Solanum tuberosum	chr01	4	CH_stu_158	11	117	0.000661393
Vitis vinifera	chr16	1	CH_vvi_234	5	7	0.000144716
Vitis vinifera	chr16	2	CH_vvi_319	5	7	0.000419462

Available child term results

GO term	Description	Number of clusters
GO:0000096	sulfur amino acid metabolic process	2
GO:0000162	tryptophan biosynthetic process	1
GO:0006418	tRNA aminoacylation for protein translation	4
GO:0006419	alanyl-tRNA aminoacylation	9
GO:0006420	arginyl-tRNA aminoacylation	11
GO:0006421	asparaginyl-tRNA aminoacylation	6
GO:0006423	cysteinyl-tRNA aminoacylation	12
GO:0006426	glycyl-tRNA aminoacylation	15
GO:0006428	isoleucyl-tRNA aminoacylation	5
GO:0006429	leucyl-tRNA aminoacylation	8
GO:0006430	lysyl-tRNA aminoacylation	11
GO:0006431	methionyl-tRNA aminoacylation	4
GO:0006432	phenylalanyl-tRNA aminoacylation	2
GO:0006433	prolyl-tRNA aminoacylation	7
GO:0006434	seryl-tRNA aminoacylation	16
GO:0006435	threonyl-tRNA aminoacylation	5
GO:0006436	tryptophanyl-tRNA aminoacylation	6
GO:0006438	valyl-tRNA aminoacylation	29
GO:0006527	arginine catabolic process	1
GO:0006529	asparagine biosynthetic process	4
GO:0006535	cysteine biosynthetic process from serine	12
GO:0006536	glutamate metabolic process	2
GO:0006540	glutamate decarboxylation to succinate	2
GO:0006541	glutamine metabolic process	3
GO:0006542	glutamine biosynthetic process	8
GO:0006552	leucine catabolic process	1
GO:0006556	S-adenosylmethionine biosynthetic process	3
GO:0006559	L-phenylalanine catabolic process	26
GO:0006560	proline metabolic process	2
GO:0006562	proline catabolic process	3
GO:0006567	threonine catabolic process	2
GO:0006568	tryptophan metabolic process	1
GO:0006569	tryptophan catabolic process	20
GO:0006571	tyrosine biosynthetic process	9
GO:0006572	tyrosine catabolic process	4
GO:0006574	valine catabolic process	3
GO:0006575	cellular modified amino acid metabolic process	2
GO:0006591	ornithine metabolic process	12
GO:0006760	folic acid-containing compound metabolic process	6
GO:0008612	peptidyl-lysine modification to hypusine	3
GO:0008652	cellular amino acid biosynthetic process	5
GO:0009067	aspartate family amino acid biosynthetic process	1
GO:0009072	aromatic amino acid family metabolic process	1
GO:0009098	leucine biosynthetic process	1
GO:0018920	glyphosate metabolic process	1
GO:0019281	L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine	1
GO:0019447	D-cysteine catabolic process	1
GO:0019450	L-cysteine catabolic process to pyruvate	6
GO:0019464	glycine decarboxylation via glycine cleavage system	3
GO:0019509	L-methionine salvage from methylthioadenosine	14
GO:0030328	prenylcysteine catabolic process	4
GO:0031336	negative regulation of sulfur amino acid metabolic process	4
GO:0033387	putrescine biosynthetic process from ornithine	8
GO:0033388	putrescine biosynthetic process from arginine	2
GO:0033506	glucosinolate biosynthetic process from homomethionine	4
GO:0042450	arginine biosynthetic process via ornithine	1
GO:0046900	tetrahydrofolylpolyglutamate metabolic process	6
GO:0046901	tetrahydrofolylpolyglutamate biosynthetic process	4
GO:0071266	'de novo' L-methionine biosynthetic process	9
GO:1901605	alpha-amino acid metabolic process	4
GO:1901607	alpha-amino acid biosynthetic process	11

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