PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0044271
Description: cellular nitrogen compound biosynthetic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Citrus sinensis	scaffold00037	1	CH_csi_147	5	7	0.000656254
Eucalyptus grandis	scaffold_9	3	CH_egr_724	17	74	0.000119203
Eucalyptus grandis	scaffold_9	6	CH_egr_286	17	74	0.000119203
Populus trichocarpa	Chr02	5	CH_ptr_98	10	37	0.0000744503
Populus trichocarpa	Chr02	6	CH_ptr_126	15	49	0.000108422
Theobroma cacao	scaffold_8	3	CH_tca_336	16	70	0.00018379
Theobroma cacao	scaffold_8	6	CH_tca_108	16	70	0.00018379

Available child term results

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0000162	tryptophan biosynthetic process	1
GO:0006065	UDP-glucuronate biosynthetic process	5
GO:0006164	purine nucleotide biosynthetic process	1
GO:0006169	adenosine salvage	4
GO:0006177	GMP biosynthetic process	2
GO:0006182	cGMP biosynthetic process	27
GO:0006183	GTP biosynthetic process	11
GO:0006223	uracil salvage	2
GO:0006231	dTMP biosynthetic process	7
GO:0006233	dTDP biosynthetic process	3
GO:0006269	DNA replication, synthesis of RNA primer	8
GO:0006351	transcription, DNA-templated	38
GO:0006352	DNA-dependent transcription, initiation	11
GO:0006353	DNA-dependent transcription, termination	6
GO:0006354	DNA-dependent transcription, elongation	12
GO:0006355	regulation of transcription, DNA-dependent	118
GO:0006357	regulation of transcription from RNA polymerase II promoter	4
GO:0006366	transcription from RNA polymerase II promoter	3
GO:0006367	transcription initiation from RNA polymerase II promoter	12
GO:0006383	transcription from RNA polymerase III promoter	7
GO:0006529	asparagine biosynthetic process	4
GO:0006556	S-adenosylmethionine biosynthetic process	3
GO:0006557	S-adenosylmethioninamine biosynthetic process	3
GO:0006596	polyamine biosynthetic process	8
GO:0006597	spermine biosynthetic process	10
GO:0006741	NADP biosynthetic process	20
GO:0006784	heme a biosynthetic process	3
GO:0006809	nitric oxide biosynthetic process	2
GO:0008615	pyridoxine biosynthetic process	1
GO:0008616	queuosine biosynthetic process	8
GO:0009190	cyclic nucleotide biosynthetic process	1
GO:0009236	cobalamin biosynthetic process	5
GO:0009301	snRNA transcription	4
GO:0009435	NAD biosynthetic process	1
GO:0009446	putrescine biosynthetic process	1
GO:0009759	indole glucosinolate biosynthetic process	55
GO:0009821	alkaloid biosynthetic process	6
GO:0010024	phytochromobilin biosynthetic process	2
GO:0015986	ATP synthesis coupled proton transport	7
GO:0019277	UDP-N-acetylgalactosamine biosynthetic process	1
GO:0019305	dTDP-rhamnose biosynthetic process	2
GO:0019354	siroheme biosynthetic process	1
GO:0019358	nicotinate nucleotide salvage	2
GO:0019428	allantoin biosynthetic process	2
GO:0030418	nicotianamine biosynthetic process	11
GO:0031564	transcription antitermination	2
GO:0031935	regulation of chromatin silencing	6
GO:0032774	RNA biosynthetic process	11
GO:0032784	regulation of DNA-dependent transcription, elongation	11
GO:0032786	positive regulation of DNA-dependent transcription, elongation	1
GO:0033387	putrescine biosynthetic process from ornithine	8
GO:0033388	putrescine biosynthetic process from arginine	2
GO:0033466	trans-zeatin biosynthetic process	4
GO:0034654	nucleobase-containing compound biosynthetic process	7
GO:0036172	thiamine salvage	2
GO:0042318	penicillin biosynthetic process	2
GO:0042351	'de novo' GDP-L-fucose biosynthetic process	2
GO:0043100	pyrimidine nucleobase salvage	4
GO:0044205	'de novo' UMP biosynthetic process	8
GO:0045014	negative regulation of transcription by glucose	2
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045893	positive regulation of transcription, DNA-dependent	4
GO:0046084	adenine biosynthetic process	1
GO:0046901	tetrahydrofolylpolyglutamate biosynthetic process	4
GO:0046938	phytochelatin biosynthetic process	22
GO:0048034	heme O biosynthetic process	5
GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	7
GO:0080028	nitrile biosynthetic process	33
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8
GO:1901183	positive regulation of camalexin biosynthetic process	2
GO:2001295	malonyl-CoA biosynthetic process	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