PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0019538
Description: protein metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00061	6	CH_atr_67	10	12	0.0000547587
Eucalyptus grandis	scaffold_4	4	CH_egr_92	39	73	0.00000000000000535642
Eucalyptus grandis	scaffold_8	4	CH_egr_110	50	128	0.0000000000011545
Eucalyptus grandis	scaffold_4	5	CH_egr_108	39	73	0.000000000000127075
Eucalyptus grandis	scaffold_4	6	CH_egr_115	42	73	0.0000000000000071205
Fragaria vesca	LG7	3	CH_fve_287	12	17	0.0000898474
Fragaria vesca	LG7	6	CH_fve_85	12	17	0.0000898474
Lotus japonicus	chr3	4	CH_lja_11	10	20	0.0000413877
Lotus japonicus	chr3	5	CH_lja_17	10	20	0.000203695
Lotus japonicus	chr2	6	CH_lja_34	10	19	0.000512123
Medicago truncatula	chr5	1	CH_mtr_471	10	18	0.000253406
Medicago truncatula	chr5	2	CH_mtr_679	10	18	0.000751708
Medicago truncatula	chr5	4	CH_mtr_181	10	18	0.000253406
Medicago truncatula	chr5	5	CH_mtr_226	10	18	0.000751708
Oryza sativa ssp. japonica	10	1	CH_osa_152	27	78	0.000000259092
Oryza sativa ssp. japonica	10	2	CH_osa_169	27	78	0.00000107496
Oryza sativa ssp. japonica	10	3	CH_osa_136	21	38	0.0000000269742
Oryza sativa ssp. japonica	10	4	CH_osa_72	28	82	0.000000153675
Oryza sativa ssp. japonica	7	4	CH_osa_165	11	19	0.000898298
Oryza sativa ssp. japonica	10	5	CH_osa_87	28	82	0.00000066833
Oryza sativa ssp. japonica	10	6	CH_osa_86	21	38	0.0000000269742
Prunus persica	scaffold_3	6	CH_ppe_105	86	300	0.00000195973
Solanum lycopersicum	ch03	1	CH_sly_292	23	62	0.000066238
Solanum lycopersicum	ch03	2	CH_sly_435	23	62	0.000472803
Solanum tuberosum	chr07	6	CH_stu_118	15	16	0.00000000385789

Available child term results

GO term	Description	Number of clusters
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	6
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:0006508	proteolysis	27
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:0008213	protein alkylation	1
GO:0008612	peptidyl-lysine modification to hypusine	3
GO:0009101	glycoprotein biosynthetic process	13
GO:0010452	histone H3-K36 methylation	2
GO:0010731	protein glutathionylation	16
GO:0016255	attachment of GPI anchor to protein	38
GO:0016540	protein autoprocessing	10
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: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:0030163	protein catabolic process	2
GO:0031145	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process	8
GO:0031365	N-terminal protein amino acid modification	6
GO:0034968	histone lysine methylation	1
GO:0034975	protein folding in endoplasmic reticulum	8
GO:0035067	negative regulation of histone acetylation	8
GO:0035278	negative regulation of translation involved in gene silencing by miRNA	18
GO:0035335	peptidyl-tyrosine dephosphorylation	2
GO:0042026	protein refolding	5
GO:0042157	lipoprotein metabolic process	2
GO:0042176	regulation of protein catabolic process	6
GO:0042177	negative regulation of protein catabolic process	2
GO:0042964	thioredoxin biosynthetic process	6
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	3
GO:0043335	protein unfolding	2
GO:0043967	histone H4 acetylation	6
GO:0043968	histone H2A acetylation	4
GO:0044257	cellular protein catabolic process	35
GO:0044267	cellular protein metabolic process	22
GO:0045116	protein neddylation	4
GO:0045900	negative regulation of translational elongation	3
GO:0045901	positive regulation of translational elongation	3
GO:0051085	chaperone mediated protein folding requiring cofactor	2
GO:0051444	negative regulation of ubiquitin-protein ligase activity	4
GO:0051603	proteolysis involved in cellular protein catabolic process	6
GO:0061077	chaperone-mediated protein folding	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:0071586	CAAX-box protein processing	3
GO:0071900	regulation of protein serine/threonine kinase activity	2
GO:0090042	tubulin deacetylation	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