PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0044260
Description: cellular macromolecule metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00010	9	CH_atr_19	22	59	0.000978188
Amborella trichopoda	scaffold00010	12	CH_atr_6	22	59	0.000978188
Arabidopsis thaliana	3	5	CH_ath_124	112	280	0.000275646
Arabidopsis thaliana	3	6	CH_ath_134	116	280	0.000341729
Carica papaya	supercontig_7	3	CH_cpa_300	30	67	0.000507897
Carica papaya	supercontig_7	6	CH_cpa_29	34	74	0.0000261456
Carica papaya	supercontig_1	11	CH_cpa_2	12	21	0.000819746
Chlamydomonas reinhardtii	chromosome_1	2	CH_cre_66	12	17	0.000484165
Chlamydomonas reinhardtii	chromosome_1	5	CH_cre_17	12	17	0.000484165
Citrullus lanatus	Chr3	3	CH_cla_334	28	61	0.000900447
Cucumis melo	CM3.5_scaffold00001	1	CH_cme_165	22	65	0.000279345
Cucumis melo	CM3.5_scaffold00047	3	CH_cme_296	17	26	0.000309129
Cucumis melo	CM3.5_scaffold00047	6	CH_cme_60	17	26	0.000309129
Eucalyptus grandis	scaffold_2	2	CH_egr_749	30	75	0.000451091
Eucalyptus grandis	scaffold_7	2	CH_egr_748	20	38	0.000426455
Eucalyptus grandis	scaffold_7	5	CH_egr_275	20	38	0.000426455
Fragaria vesca	LG3	1	CH_fve_92	15	22	0.000000170206
Fragaria vesca	LG3	2	CH_fve_144	15	22	0.00000395942
Fragaria vesca	LG3	4	CH_fve_28	15	22	0.000000170206
Fragaria vesca	LG3	5	CH_fve_39	15	22	0.00000395942
Gossypium raimondii	Chr11	1	CH_gra_64	19	22	0.0000000000675161
Gossypium raimondii	Chr11	2	CH_gra_92	19	22	0.00000000231571
Gossypium raimondii	Chr11	4	CH_gra_42	19	22	0.0000000000675161
Gossypium raimondii	Chr11	5	CH_gra_47	19	22	0.00000000231571
Lotus japonicus	chr2	3	CH_lja_37	26	55	0.0000000519549
Lotus japonicus	chr2	6	CH_lja_7	26	55	0.0000000519549
Lotus japonicus	chr4	9	CH_lja_17	23	82	0.000914877
Lotus japonicus	chr4	12	CH_lja_9	26	98	0.000519694
Manihot esculenta	scaffold06039	1	CH_mes_175	10	13	0.000907851
Manihot esculenta	scaffold03569	2	CH_mes_191	9	9	0.000338175
Manihot esculenta	scaffold06039	4	CH_mes_22	10	13	0.000907851
Prunus persica	scaffold_4	4	CH_ppe_58	18	25	0.0000000224796
Prunus persica	scaffold_4	5	CH_ppe_75	18	25	0.000000689091
Prunus persica	scaffold_4	6	CH_ppe_133	92	300	0.0000761691
Ricinus communis	30128	1	CH_rco_202	12	19	0.00071437
Ricinus communis	30128	4	CH_rco_34	12	19	0.00071437
Solanum lycopersicum	ch11	3	CH_sly_289	13	13	0.00000361381
Solanum lycopersicum	ch11	6	CH_sly_103	13	13	0.00000361381
Solanum tuberosum	chr11	1	CH_stu_341	11	13	0.0000367276
Solanum tuberosum	chr11	3	CH_stu_459	13	13	0.00000564869
Solanum tuberosum	chr11	4	CH_stu_131	11	13	0.0000367276
Solanum tuberosum	chr11	6	CH_stu_160	13	13	0.00000564869
Theobroma cacao	scaffold_10r	3	CH_tca_439	17	24	0.000707593
Theobroma cacao	scaffold_10r	4	CH_tca_79	12	18	0.000558647

Available child term results

GO term	Description	Number of clusters
GO:0000012	single strand break repair	2
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	6
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:0000712	resolution of meiotic recombination intermediates	5
GO:0000723	telomere maintenance	16
GO:0000724	double-strand break repair via homologous recombination	9
GO:0000966	RNA 5'-end processing	12
GO:0001510	RNA methylation	1
GO:0001682	tRNA 5'-leader removal	4
GO:0001881	receptor recycling	2
GO:0002098	tRNA wobble uridine modification	1
GO:0006073	cellular glucan metabolic process	2
GO:0006075	(1->3)-beta-D-glucan biosynthetic process	36
GO:0006259	DNA metabolic process	85
GO:0006260	DNA replication	4
GO:0006269	DNA replication, synthesis of RNA primer	8
GO:0006271	DNA strand elongation involved in DNA replication	2
GO:0006278	RNA-dependent DNA replication	14
GO:0006279	premeiotic DNA replication	2
GO:0006281	DNA repair	5
GO:0006282	regulation of DNA repair	5
GO:0006284	base-excision repair	8
GO:0006294	nucleotide-excision repair, preincision complex assembly	2
GO:0006298	mismatch repair	7
GO:0006302	double-strand break repair	1
GO:0006303	double-strand break repair via nonhomologous end joining	12
GO:0006306	DNA methylation	5
GO:0006308	DNA catabolic process	16
GO:0006310	DNA recombination	48
GO:0006312	mitotic recombination	2
GO:0006323	DNA packaging	11
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:0006412	translation	6
GO:0006413	translational initiation	3
GO:0006414	translational elongation	11
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:0006450	regulation of translational fidelity	4
GO:0006457	protein folding	11
GO:0006464	cellular protein modification process	69
GO:0006465	signal peptide processing	3
GO:0006468	protein phosphorylation	374
GO:0006470	protein dephosphorylation	3
GO:0006471	protein ADP-ribosylation	9
GO:0006486	protein glycosylation	5
GO:0006499	N-terminal protein myristoylation	4
GO:0006511	ubiquitin-dependent protein catabolic process	84
GO:0006515	misfolded or incompletely synthesized protein catabolic process	5
GO:0006516	glycoprotein catabolic process	2
GO:0006517	protein deglycosylation	14
GO:0006627	protein processing involved in protein targeting to mitochondrion	3
GO:0007076	mitotic chromosome condensation	4
GO:0008033	tRNA processing	40
GO:0008213	protein alkylation	1
GO:0008380	RNA splicing	1
GO:0008612	peptidyl-lysine modification to hypusine	3
GO:0008616	queuosine biosynthetic process	8
GO:0009101	glycoprotein biosynthetic process	13
GO:0009244	lipopolysaccharide core region biosynthetic process	3
GO:0009250	glucan biosynthetic process	6
GO:0009252	peptidoglycan biosynthetic process	5
GO:0009301	snRNA transcription	4
GO:0009452	7-methylguanosine RNA capping	1
GO:0010032	meiotic chromosome condensation	3
GO:0010246	rhamnogalacturonan I biosynthetic process	4
GO:0010411	xyloglucan metabolic process	8
GO:0010424	DNA methylation on cytosine within a CG sequence	4
GO:0010452	histone H3-K36 methylation	2
GO:0010731	protein glutathionylation	16
GO:0015074	DNA integration	46
GO:0016070	RNA metabolic process	3
GO:0016072	rRNA metabolic process	1
GO:0016075	rRNA catabolic process	1
GO:0016180	snRNA processing	1
GO:0016255	attachment of GPI anchor to protein	38
GO:0016444	somatic cell DNA recombination	6
GO:0016556	mRNA modification	2
GO:0016567	protein ubiquitination	32
GO:0016572	histone phosphorylation	3
GO:0016575	histone deacetylation	1
GO:0016579	protein deubiquitination	1
GO:0016598	protein arginylation	3
GO:0016998	cell wall macromolecule catabolic process	29
GO:0017148	negative regulation of translation	1
GO:0017182	peptidyl-diphthamide metabolic process	3
GO:0017186	peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase	2
GO:0018023	peptidyl-lysine trimethylation	3
GO:0018149	peptide cross-linking	25
GO:0018279	protein N-linked glycosylation via asparagine	2
GO:0018282	metal incorporation into metallo-sulfur cluster	2
GO:0018298	protein-chromophore linkage	5
GO:0018343	protein farnesylation	6
GO:0030244	cellulose biosynthetic process	2
GO:0030245	cellulose catabolic process	3
GO:0031054	pre-miRNA processing	2
GO:0031123	RNA 3'-end processing	2
GO:0031145	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process	8
GO:0031167	rRNA methylation	5
GO:0031365	N-terminal protein amino acid modification	6
GO:0031425	chloroplast RNA processing	2
GO:0031497	chromatin assembly	23
GO:0031507	heterochromatin assembly	1
GO:0031564	transcription antitermination	2
GO:0031935	regulation of chromatin silencing	6
GO:0032508	DNA duplex unwinding	3
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:0032877	positive regulation of DNA endoreduplication	2
GO:0032951	regulation of beta-glucan biosynthetic process	6
GO:0032953	regulation of (1->3)-beta-D-glucan biosynthetic process	2
GO:0033567	DNA replication, Okazaki fragment processing	6
GO:0033692	cellular polysaccharide biosynthetic process	1
GO:0034227	tRNA thio-modification	4
GO:0034470	ncRNA processing	4
GO:0034645	cellular macromolecule biosynthetic process	23
GO:0034660	ncRNA metabolic process	3
GO:0034968	histone lysine methylation	1
GO:0034975	protein folding in endoplasmic reticulum	8
GO:0035067	negative regulation of histone acetylation	8
GO:0035196	production of miRNAs involved in gene silencing by miRNA	2
GO:0035278	negative regulation of translation involved in gene silencing by miRNA	18
GO:0035279	mRNA cleavage involved in gene silencing by miRNA	6
GO:0035335	peptidyl-tyrosine dephosphorylation	2
GO:0042026	protein refolding	5
GO:0042779	tRNA 3'-trailer cleavage	1
GO:0042964	thioredoxin biosynthetic process	6
GO:0043144	snoRNA processing	1
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	3
GO:0043247	telomere maintenance in response to DNA damage	8
GO:0043335	protein unfolding	2
GO:0043967	histone H4 acetylation	6
GO:0043968	histone H2A acetylation	4
GO:0044030	regulation of DNA methylation	11
GO:0044036	cell wall macromolecule metabolic process	3
GO:0044257	cellular protein catabolic process	35
GO:0044264	cellular polysaccharide metabolic process	5
GO:0044265	cellular macromolecule catabolic process	2
GO:0044267	cellular protein metabolic process	22
GO:0045014	negative regulation of transcription by glucose	2
GO:0045116	protein neddylation	4
GO:0045128	negative regulation of reciprocal meiotic recombination	4
GO:0045226	extracellular polysaccharide biosynthetic process	2
GO:0045292	mRNA cis splicing, via spliceosome	8
GO:0045493	xylan catabolic process	2
GO:0045739	positive regulation of DNA repair	2
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045893	positive regulation of transcription, DNA-dependent	4
GO:0045900	negative regulation of translational elongation	3
GO:0045901	positive regulation of translational elongation	3
GO:0045910	negative regulation of DNA recombination	2
GO:0048024	regulation of mRNA splicing, via spliceosome	2
GO:0051085	chaperone mediated protein folding requiring cofactor	2
GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	7
GO:0051103	DNA ligation involved in DNA repair	11
GO:0051254	positive regulation of RNA metabolic process	1
GO:0051274	beta-glucan biosynthetic process	2
GO:0051444	negative regulation of ubiquitin-protein ligase activity	4
GO:0051603	proteolysis involved in cellular protein catabolic process	6
GO:0051973	positive regulation of telomerase activity	4
GO:0052541	plant-type cell wall cellulose metabolic process	2
GO:0061077	chaperone-mediated protein folding	2
GO:0070526	threonylcarbamoyladenosine biosynthetic process	2
GO:0070647	protein modification by small protein conjugation or removal	1
GO:0070734	histone H3-K27 methylation	4
GO:0070932	histone H3 deacetylation	1
GO:0071076	RNA 3' uridylation	4
GO:0071103	DNA conformation change	7
GO:0071586	CAAX-box protein processing	3
GO:0071900	regulation of protein serine/threonine kinase activity	2
GO:0080156	mitochondrial mRNA modification	2
GO:0090042	tubulin deacetylation	2
GO:0090296	regulation of mitochondrial DNA replication	3
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8
GO:1900363	regulation of mRNA polyadenylation	2
GO:1900865	chloroplast RNA modification	1
GO:2000112	regulation of cellular macromolecule biosynthetic process	8
GO:2000113	negative regulation of cellular macromolecule biosynthetic process	2

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