PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0016070
Description: RNA metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Solanum lycopersicum	ch01	4	CH_sly_88	16	126	0.000106256
Solanum lycopersicum	ch06	6	CH_sly_148	12	29	0.000216897
Solanum tuberosum	chr10	2	CH_stu_566	6	10	0.000779334

Available child term results

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0000154	rRNA modification	42
GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
GO:0000244	spliceosomal tri-snRNP complex assembly	6
GO:0000245	spliceosomal complex assembly	6
GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	6
GO:0000387	spliceosomal snRNP assembly	3
GO:0000966	RNA 5'-end processing	12
GO:0001510	RNA methylation	1
GO:0001682	tRNA 5'-leader removal	4
GO:0002098	tRNA wobble uridine modification	1
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:0006364	rRNA processing	6
GO:0006366	transcription from RNA polymerase II promoter	3
GO:0006367	transcription initiation from RNA polymerase II promoter	12
GO:0006370	7-methylguanosine mRNA capping	5
GO:0006376	mRNA splice site selection	1
GO:0006378	mRNA polyadenylation	2
GO:0006383	transcription from RNA polymerase III promoter	7
GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	3
GO:0006396	RNA processing	12
GO:0006397	mRNA processing	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:0008033	tRNA processing	40
GO:0008380	RNA splicing	1
GO:0008616	queuosine biosynthetic process	8
GO:0009301	snRNA transcription	4
GO:0009452	7-methylguanosine RNA capping	1
GO:0016072	rRNA metabolic process	1
GO:0016075	rRNA catabolic process	1
GO:0016180	snRNA processing	1
GO:0016556	mRNA modification	2
GO:0031054	pre-miRNA processing	2
GO:0031123	RNA 3'-end processing	2
GO:0031167	rRNA methylation	5
GO:0031425	chloroplast RNA processing	2
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:0034227	tRNA thio-modification	4
GO:0034470	ncRNA processing	4
GO:0034660	ncRNA metabolic process	3
GO:0035196	production of miRNAs involved in gene silencing by miRNA	2
GO:0035279	mRNA cleavage involved in gene silencing by miRNA	6
GO:0042779	tRNA 3'-trailer cleavage	1
GO:0043144	snoRNA processing	1
GO:0045014	negative regulation of transcription by glucose	2
GO:0045292	mRNA cis splicing, via spliceosome	8
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045893	positive regulation of transcription, DNA-dependent	4
GO:0048024	regulation of mRNA splicing, via spliceosome	2
GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	7
GO:0051254	positive regulation of RNA metabolic process	1
GO:0070526	threonylcarbamoyladenosine biosynthetic process	2
GO:0071076	RNA 3' uridylation	4
GO:0080156	mitochondrial mRNA modification	2
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8
GO:1900363	regulation of mRNA polyadenylation	2
GO:1900865	chloroplast RNA modification	1

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