PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0006796
Description: phosphate-containing compound metabolic process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00106	6	CH_atr_45	11	13	0.0000000160423
Citrus sinensis	scaffold00136	1	CH_csi_71	10	12	0.00000122487
Citrus sinensis	scaffold00136	4	CH_csi_18	10	12	0.00000122487
Citrus sinensis	scaffold00136	5	CH_csi_20	10	12	0.00000273149
Citrus sinensis	scaffold00136	6	CH_csi_29	10	12	0.0000103245
Cucumis melo	CM3.5_scaffold00001	1	CH_cme_110	16	55	0.0000417516
Cucumis melo	CM3.5_scaffold00001	2	CH_cme_131	18	64	0.0000385581
Cucumis melo	CM3.5_scaffold00001	3	CH_cme_295	18	64	0.000297615
Cucumis melo	CM3.5_scaffold00001	4	CH_cme_31	16	55	0.0000417516
Cucumis melo	CM3.5_scaffold00001	5	CH_cme_34	18	64	0.0000385581
Cucumis melo	CM3.5_scaffold00001	6	CH_cme_59	18	64	0.000297615
Eucalyptus grandis	scaffold_3	4	CH_egr_223	33	138	0.000159411
Fragaria vesca	LG2	1	CH_fve_218	16	65	0.000226523
Fragaria vesca	LG2	4	CH_fve_53	16	65	0.000226523
Glycine max	Gm15	4	CH_gma_56	10	14	0.000039341
Glycine max	Gm15	5	CH_gma_68	10	14	0.0000797112
Malus domestica	10	6	CH_mdo_59	41	272	0.000587842
Medicago truncatula	chr5	1	CH_mtr_156	20	68	0.00000000229126
Medicago truncatula	chr8	1	CH_mtr_373	17	77	0.0000276241
Medicago truncatula	chr5	2	CH_mtr_206	20	68	0.00000000868707
Medicago truncatula	chr8	2	CH_mtr_479	17	77	0.0000819497
Medicago truncatula	chr5	3	CH_mtr_167	24	68	0.0000000000334814
Medicago truncatula	chr5	4	CH_mtr_87	20	68	0.00000000229126
Medicago truncatula	chr8	4	CH_mtr_155	17	77	0.0000276241
Medicago truncatula	chr5	5	CH_mtr_95	20	68	0.00000000868707
Medicago truncatula	chr8	5	CH_mtr_172	17	77	0.0000819497
Medicago truncatula	chr5	6	CH_mtr_93	24	68	0.0000000000334814
Prunus persica	scaffold_4	6	CH_ppe_100	23	65	0.000000939635
Solanum tuberosum	chr07	1	CH_stu_196	12	16	0.0000000349017
Solanum tuberosum	chr07	3	CH_stu_181	16	19	0.0000000000113061
Solanum tuberosum	chr07	4	CH_stu_95	12	16	0.0000000349017
Solanum tuberosum	chr07	6	CH_stu_93	16	19	0.0000000000113061
Theobroma cacao	scaffold_1	4	CH_tca_61	10	17	0.0000570471
Theobroma cacao	scaffold_1	5	CH_tca_67	10	17	0.000122896
Theobroma cacao	scaffold_1	6	CH_tca_116	10	17	0.000389055
Vitis vinifera	chr17	6	CH_vvi_135	35	176	0.000710336
Vitis vinifera	chr17	12	CH_vvi_10	27	170	0.0009565

Available child term results

GO term	Description	Number of clusters
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	6
GO:0006003	fructose 2,6-bisphosphate metabolic process	4
GO:0006065	UDP-glucuronate biosynthetic process	5
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	1
GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	2
GO:0006164	purine nucleotide biosynthetic process	1
GO:0006177	GMP biosynthetic process	2
GO:0006182	cGMP biosynthetic process	27
GO:0006183	GTP biosynthetic process	11
GO:0006184	GTP catabolic process	6
GO:0006200	ATP catabolic process	7
GO:0006231	dTMP biosynthetic process	7
GO:0006233	dTDP biosynthetic process	3
GO:0006468	protein phosphorylation	374
GO:0006470	protein dephosphorylation	3
GO:0006505	GPI anchor metabolic process	2
GO:0006656	phosphatidylcholine biosynthetic process	4
GO:0006741	NADP biosynthetic process	20
GO:0009051	pentose-phosphate shunt, oxidative branch	2
GO:0009052	pentose-phosphate shunt, non-oxidative branch	3
GO:0009117	nucleotide metabolic process	1
GO:0009166	nucleotide catabolic process	1
GO:0009190	cyclic nucleotide biosynthetic process	1
GO:0009205	purine ribonucleoside triphosphate metabolic process	2
GO:0009225	nucleotide-sugar metabolic process	6
GO:0009435	NAD biosynthetic process	1
GO:0010322	regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	2
GO:0015965	diadenosine tetraphosphate metabolic process	3
GO:0015969	guanosine tetraphosphate metabolic process	1
GO:0015986	ATP synthesis coupled proton transport	7
GO:0016255	attachment of GPI anchor to protein	38
GO:0016310	phosphorylation	13
GO:0016311	dephosphorylation	4
GO:0016572	histone phosphorylation	3
GO:0019220	regulation of phosphate metabolic process	1
GO:0019277	UDP-N-acetylgalactosamine biosynthetic process	1
GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	9
GO:0019305	dTDP-rhamnose biosynthetic process	2
GO:0019358	nicotinate nucleotide salvage	2
GO:0032312	regulation of ARF GTPase activity	3
GO:0032313	regulation of Rab GTPase activity	3
GO:0033356	UDP-L-arabinose metabolic process	2
GO:0035335	peptidyl-tyrosine dephosphorylation	2
GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process	6
GO:0042325	regulation of phosphorylation	1
GO:0042327	positive regulation of phosphorylation	1
GO:0042351	'de novo' GDP-L-fucose biosynthetic process	2
GO:0042773	ATP synthesis coupled electron transport	5
GO:0043647	inositol phosphate metabolic process	2
GO:0044205	'de novo' UMP biosynthetic process	8
GO:0045337	farnesyl diphosphate biosynthetic process	6
GO:0045980	negative regulation of nucleotide metabolic process	3
GO:0046033	AMP metabolic process	4
GO:0046034	ATP metabolic process	4
GO:0046443	FAD metabolic process	1
GO:0046473	phosphatidic acid metabolic process	2
GO:0046488	phosphatidylinositol metabolic process	2
GO:0046496	nicotinamide nucleotide metabolic process	3
GO:0046854	phosphatidylinositol phosphorylation	3
GO:0046856	phosphatidylinositol dephosphorylation	4
GO:0046939	nucleotide phosphorylation	2
GO:0052746	inositol phosphorylation	4
GO:0071900	regulation of protein serine/threonine kinase activity	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