PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0019752
Description: carboxylic acid metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Beta vulgaris	Bvchr3.sca006	2	CH_bvu_222	11	39	0.000235515
Beta vulgaris	Bvchr3.sca006	5	CH_bvu_36	11	39	0.000235515
Glycine max	Gm08	4	CH_gma_50	10	31	0.00000455568
Glycine max	Gm08	5	CH_gma_49	13	34	0.000000193778
Solanum lycopersicum	ch08	3	CH_sly_46	17	22	2.56789e-18
Solanum lycopersicum	ch08	5	CH_sly_36	16	22	6.91122e-17
Solanum lycopersicum	ch08	6	CH_sly_39	17	22	2.56789e-18
Solanum tuberosum	chr08	2	CH_stu_109	21	65	0.000000000000631267
Solanum tuberosum	chr08	3	CH_stu_122	23	65	0.0000000000000203093
Solanum tuberosum	chr08	5	CH_stu_59	26	103	0.0000000000000953827
Solanum tuberosum	chr08	6	CH_stu_77	28	103	0.0000000000000100413
Solanum tuberosum	chr05	7	CH_stu_6	6	14	0.00017748

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:0001561	fatty acid alpha-oxidation	13
GO:0006065	UDP-glucuronate biosynthetic process	5
GO:0006083	acetate metabolic process	2
GO:0006086	acetyl-CoA biosynthetic process from pyruvate	3
GO:0006097	glyoxylate cycle	3
GO:0006101	citrate metabolic process	3
GO:0006102	isocitrate metabolic process	2
GO:0006106	fumarate metabolic process	11
GO:0006108	malate metabolic process	2
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:0006520	cellular amino acid metabolic process	5
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:0006631	fatty acid metabolic process	8
GO:0006633	fatty acid biosynthetic process	40
GO:0006635	fatty acid beta-oxidation	3
GO:0006636	unsaturated fatty acid biosynthetic process	3
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:0009423	chorismate biosynthetic process	1
GO:0009696	salicylic acid metabolic process	2
GO:0009697	salicylic acid biosynthetic process	42
GO:0010322	regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	2
GO:0010371	regulation of gibberellin biosynthetic process	2
GO:0010373	negative regulation of gibberellin biosynthetic process	2
GO:0010430	fatty acid omega-oxidation	4
GO:0010597	green leaf volatile biosynthetic process	32
GO:0018874	benzoate metabolic process	4
GO:0018920	glyphosate metabolic process	1
GO:0019281	L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine	1
GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	9
GO:0019370	leukotriene biosynthetic process	7
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:0019605	butyrate metabolic process	6
GO:0019632	shikimate metabolic process	2
GO:0030328	prenylcysteine catabolic process	4
GO:0030418	nicotianamine biosynthetic process	11
GO:0030497	fatty acid elongation	4
GO:0031336	negative regulation of sulfur amino acid metabolic process	4
GO:0031408	oxylipin biosynthetic process	12
GO:0032787	monocarboxylic acid metabolic process	3
GO:0033387	putrescine biosynthetic process from ornithine	8
GO:0033388	putrescine biosynthetic process from arginine	2
GO:0033473	indoleacetic acid conjugate metabolic process	2
GO:0033506	glucosinolate biosynthetic process from homomethionine	4
GO:0033587	shikimate biosynthetic process	4
GO:0042318	penicillin biosynthetic process	2
GO:0042450	arginine biosynthetic process via ornithine	1
GO:0046345	abscisic acid catabolic process	28
GO:0046394	carboxylic acid biosynthetic process	2
GO:0046417	chorismate metabolic process	2
GO:0046459	short-chain fatty acid metabolic process	2
GO:0046900	tetrahydrofolylpolyglutamate metabolic process	6
GO:0046901	tetrahydrofolylpolyglutamate biosynthetic process	4
GO:0051791	medium-chain fatty acid metabolic process	4
GO:0071266	'de novo' L-methionine biosynthetic process	9
GO:0080024	indolebutyric acid metabolic process	3
GO:0080142	regulation of salicylic acid biosynthetic process	7
GO:0090359	negative regulation of abscisic acid biosynthetic process	6
GO:1901605	alpha-amino acid metabolic process	4
GO:1901607	alpha-amino acid biosynthetic process	11
GO:2000082	regulation of L-ascorbic acid biosynthetic process	2
GO:2000083	negative regulation of L-ascorbic acid biosynthetic process	40

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