PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0006464
Description: cellular protein modification process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Beta vulgaris	Bvchr2_un.sca002	1	CH_bvu_45	10	10	0.00000000173225
Beta vulgaris	Bvchr9.sca026	1	CH_bvu_91	8	8	0.000000720081
Beta vulgaris	Bvchr2_un.sca002	2	CH_bvu_57	10	10	0.0000000045353
Beta vulgaris	Bvchr9.sca026	2	CH_bvu_112	8	8	0.00000155404
Beta vulgaris	Bvchr9.sca026	3	CH_bvu_153	8	8	0.00000392625
Beta vulgaris	Bvchr2_un.sca002	4	CH_bvu_12	10	10	0.00000000173225
Beta vulgaris	Bvchr2_un.sca002	5	CH_bvu_16	10	10	0.0000000045353
Beta vulgaris	Bvchr3.sca006	5	CH_bvu_46	10	20	0.000506949
Beta vulgaris	Bvchr2_un.sca002	6	CH_bvu_23	10	10	0.0000000144602
Capsella rubella	scaffold_4	5	CH_cru_81	10	18	0.000777691
Carica papaya	supercontig_124	3	CH_cpa_292	8	11	0.000391009
Citrullus lanatus	Chr9	5	CH_cla_38	10	19	0.000186221
Eucalyptus grandis	scaffold_3	1	CH_egr_551	23	79	0.000195406
Eucalyptus grandis	scaffold_7	1	CH_egr_304	20	43	0.00000010874
Eucalyptus grandis	scaffold_8	1	CH_egr_166	24	44	0.00000000000670987
Eucalyptus grandis	scaffold_7	2	CH_egr_384	21	44	0.0000000819851
Eucalyptus grandis	scaffold_8	2	CH_egr_242	24	44	0.0000000000438468
Eucalyptus grandis	scaffold_7	3	CH_egr_441	22	44	0.000000073968
Eucalyptus grandis	scaffold_7	3	CH_egr_296	30	65	0.000000000120381
Eucalyptus grandis	scaffold_7	4	CH_egr_156	20	43	0.00000010874
Eucalyptus grandis	scaffold_3	5	CH_egr_259	34	142	0.000144911
Eucalyptus grandis	scaffold_7	5	CH_egr_177	21	44	0.0000000819851
Eucalyptus grandis	scaffold_7	6	CH_egr_205	22	44	0.000000073968
Eucalyptus grandis	scaffold_8	6	CH_egr_188	13	14	0.0000000094182
Glycine max	Gm13	4	CH_gma_44	10	12	0.000000891206
Gossypium raimondii	Chr10	3	CH_gra_261	17	43	0.0000702851
Gossypium raimondii	Chr10	6	CH_gra_82	17	43	0.0000702851
Malus domestica	12	1	CH_mdo_226	12	39	0.000581938
Malus domestica	12	2	CH_mdo_138	18	71	0.0000355189
Malus domestica	12	3	CH_mdo_414	18	71	0.000879019
Malus domestica	12	4	CH_mdo_38	12	39	0.000581938
Malus domestica	4	4	CH_mdo_16	24	125	0.00000253087
Malus domestica	12	5	CH_mdo_26	18	71	0.0000355189
Malus domestica	4	5	CH_mdo_25	24	125	0.000029052
Malus domestica	12	6	CH_mdo_65	18	71	0.000879019
Medicago truncatula	chr7	3	CH_mtr_895	9	18	0.000980812
Medicago truncatula	chr3	6	CH_mtr_184	12	27	0.0000206823
Oryza sativa ssp. japonica	2	1	CH_osa_267	8	12	0.0000518046
Oryza sativa ssp. japonica	2	2	CH_osa_290	8	12	0.000103116
Oryza sativa ssp. japonica	4	2	CH_osa_267	7	8	0.0000488185
Oryza sativa ssp. japonica	2	3	CH_osa_429	8	12	0.000342416
Oryza sativa ssp. japonica	2	3	CH_osa_484	17	73	0.000836209
Oryza sativa ssp. japonica	4	3	CH_osa_376	7	8	0.000141533
Oryza sativa ssp. japonica	12	4	CH_osa_149	18	98	0.000421076
Oryza sativa ssp. japonica	2	4	CH_osa_162	13	51	0.000815365
Oryza sativa ssp. japonica	12	5	CH_osa_155	19	98	0.000260067
Oryza sativa ssp. japonica	2	5	CH_osa_171	16	73	0.000669176
Oryza sativa ssp. japonica	2	6	CH_osa_184	17	73	0.000836209
Populus trichocarpa	Chr15	1	CH_ptr_290	8	10	0.000158812
Populus trichocarpa	Chr05	2	CH_ptr_366	18	56	0.000220985
Populus trichocarpa	Chr15	2	CH_ptr_398	8	10	0.000422219
Populus trichocarpa	Chr03	3	CH_ptr_308	16	32	0.00000606369
Populus trichocarpa	Chr05	5	CH_ptr_109	18	56	0.000220985
Populus trichocarpa	Chr03	6	CH_ptr_110	16	32	0.00000606369
Populus trichocarpa	Chr12	6	CH_ptr_106	10	12	0.00000202226
Ricinus communis	30131	3	CH_rco_188	8	9	0.0000634106
Ricinus communis	30169	4	CH_rco_19	10	12	0.000000136104
Ricinus communis	30169	5	CH_rco_23	10	12	0.000000526061
Ricinus communis	30131	6	CH_rco_47	16	42	0.0000837907
Solanum tuberosum	chr01	1	CH_stu_493	18	76	0.00066638
Solanum tuberosum	chr03	3	CH_stu_468	12	19	0.00000970054
Solanum tuberosum	chr03	3	CH_stu_600	13	27	0.000164954
Solanum tuberosum	chr01	5	CH_stu_111	41	230	0.00000137742
Solanum tuberosum	chr03	6	CH_stu_174	10	13	0.0000158202
Solanum tuberosum	chr03	6	CH_stu_200	13	27	0.000164954
Vitis vinifera	chrUn	3	CH_vvi_353	12	22	0.000079989
Vitis vinifera	chr12	4	CH_vvi_83	10	17	0.000027191
Vitis vinifera	chrUn	6	CH_vvi_116	12	22	0.000079989
Vitis vinifera	chrUn	6	CH_vvi_124	25	99	0.000174159

Available child term results

GO term	Description	Number of clusters
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	6
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:0006517	protein deglycosylation	14
GO:0008213	protein alkylation	1
GO:0008612	peptidyl-lysine modification to hypusine	3
GO:0010452	histone H3-K36 methylation	2
GO:0010731	protein glutathionylation	16
GO:0016255	attachment of GPI anchor to protein	38
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: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:0031365	N-terminal protein amino acid modification	6
GO:0034968	histone lysine methylation	1
GO:0035067	negative regulation of histone acetylation	8
GO:0035335	peptidyl-tyrosine dephosphorylation	2
GO:0043967	histone H4 acetylation	6
GO:0043968	histone H2A acetylation	4
GO:0045116	protein neddylation	4
GO:0051444	negative regulation of ubiquitin-protein ligase activity	4
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: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