PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0043167
Description: ion binding

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	4	CH_ath_32	38	68	0.000000312119
Arabidopsis thaliana	5	5	CH_ath_49	38	68	0.000000433068
Arabidopsis thaliana	3	6	CH_ath_97	101	283	0.0000439466
Arabidopsis thaliana	5	6	CH_ath_50	40	68	0.000000138227
Capsella rubella	scaffold_5	4	CH_cru_43	95	288	0.000656068
Capsella rubella	scaffold_2	6	CH_cru_40	123	298	0.0000000110965
Citrullus lanatus	Chr1	4	CH_cla_23	15	16	0.000000485003
Citrullus lanatus	Chr1	5	CH_cla_26	15	16	0.00000107361
Citrullus lanatus	Chr1	6	CH_cla_41	15	16	0.000006334
Citrus sinensis	scaffold00010	2	CH_csi_113	28	46	0.0000926968
Citrus sinensis	scaffold00049	2	CH_csi_180	15	18	0.000521738
Citrus sinensis	scaffold00101	2	CH_csi_175	28	48	0.000350939
Citrus sinensis	scaffold00010	3	CH_csi_230	29	47	0.000567011
Citrus sinensis	scaffold00010	5	CH_csi_26	28	46	0.0000926968
Citrus sinensis	scaffold00049	5	CH_csi_30	15	18	0.000521738
Citrus sinensis	scaffold00101	5	CH_csi_29	28	48	0.000350939
Citrus sinensis	scaffold00010	6	CH_csi_37	29	47	0.000567011
Cucumis melo	CM3.5_scaffold00016	3	CH_cme_322	28	54	0.000587999
Cucumis melo	CM3.5_scaffold00007	4	CH_cme_22	18	23	0.000000381848
Cucumis melo	CM3.5_scaffold00007	5	CH_cme_23	18	23	0.00000092239
Cucumis melo	CM3.5_scaffold00016	6	CH_cme_64	28	54	0.000587999
Eucalyptus grandis	scaffold_6	1	CH_egr_487	23	32	0.0000557184
Eucalyptus grandis	scaffold_8	1	CH_egr_502	30	49	0.0000762869
Eucalyptus grandis	scaffold_9	1	CH_egr_382	23	29	0.00000188178
Eucalyptus grandis	scaffold_4	2	CH_egr_525	26	36	0.00000882706
Eucalyptus grandis	scaffold_9	2	CH_egr_499	23	29	0.00000394158
Eucalyptus grandis	scaffold_9	3	CH_egr_590	24	29	0.00000684968
Eucalyptus grandis	scaffold_5	4	CH_egr_214	65	151	0.0000626983
Eucalyptus grandis	scaffold_6	4	CH_egr_212	23	32	0.0000557184
Eucalyptus grandis	scaffold_9	4	CH_egr_182	23	29	0.00000188178
Eucalyptus grandis	scaffold_4	5	CH_egr_222	26	36	0.00000882706
Eucalyptus grandis	scaffold_5	5	CH_egr_266	65	151	0.000267238
Eucalyptus grandis	scaffold_9	5	CH_egr_213	23	29	0.00000394158
Eucalyptus grandis	scaffold_5	6	CH_egr_222	75	144	0.00000042955
Eucalyptus grandis	scaffold_9	6	CH_egr_246	24	29	0.00000684968
Fragaria vesca	LG3	3	CH_fve_106	30	41	0.00000000935429
Fragaria vesca	LG7	6	CH_fve_51	51	103	0.000000584663
Glycine max	Gm12	6	CH_gma_118	103	272	0.00084527
Malus domestica	10	4	CH_mdo_34	34	95	0.00040919
Malus domestica	10	5	CH_mdo_55	34	95	0.00099381
Medicago truncatula	chr2	1	CH_mtr_335	22	41	0.00000603345
Medicago truncatula	chr8	1	CH_mtr_572	29	80	0.000838091
Medicago truncatula	chr8	1	CH_mtr_236	30	63	0.000000139524
Medicago truncatula	chr2	2	CH_mtr_402	22	41	0.0000125818
Medicago truncatula	chr2	3	CH_mtr_507	24	41	0.0000168348
Medicago truncatula	chr2	4	CH_mtr_66	65	182	0.00000000000279052
Medicago truncatula	chr3	4	CH_mtr_192	55	210	0.000510372
Medicago truncatula	chr5	4	CH_mtr_124	51	163	0.00000192955
Medicago truncatula	chr8	4	CH_mtr_107	66	228	0.000000146205
Medicago truncatula	chr2	5	CH_mtr_68	66	182	0.00000000000438652
Medicago truncatula	chr3	5	CH_mtr_224	56	210	0.000710632
Medicago truncatula	chr5	5	CH_mtr_131	52	163	0.00000223035
Medicago truncatula	chr2	6	CH_mtr_69	79	184	0.0000000000000150374
Medicago truncatula	chr3	6	CH_mtr_229	66	210	0.000198266
Medicago truncatula	chr6	6	CH_mtr_259	10	10	0.000444959
Populus trichocarpa	Chr05	4	CH_ptr_79	41	79	0.00000325178
Populus trichocarpa	Chr05	4	CH_ptr_111	11	11	0.000531141
Prunus persica	scaffold_8	1	CH_ppe_260	30	53	0.0000874004
Prunus persica	scaffold_8	2	CH_ppe_304	29	49	0.0000912168
Prunus persica	scaffold_8	3	CH_ppe_314	29	43	0.0000298371
Prunus persica	scaffold_8	4	CH_ppe_79	33	58	0.0000119125
Prunus persica	scaffold_8	5	CH_ppe_85	34	58	0.00000583437
Prunus persica	scaffold_8	6	CH_ppe_121	102	249	0.0000136558
Prunus persica	scaffold_8	6	CH_ppe_104	38	60	0.00000136191
Solanum lycopersicum	ch07	1	CH_sly_79	26	30	0.0000000000101921
Solanum lycopersicum	ch07	3	CH_sly_311	18	20	0.00000535146
Solanum lycopersicum	ch07	4	CH_sly_44	26	30	0.0000000000101921
Solanum lycopersicum	ch07	6	CH_sly_108	18	20	0.00000535146
Solanum tuberosum	chr01	3	CH_stu_309	30	37	0.0000000302829
Solanum tuberosum	chr04	3	CH_stu_733	30	47	0.000537524
Solanum tuberosum	chr01	4	CH_stu_138	64	161	0.0000809205
Solanum tuberosum	chr09	4	CH_stu_34	122	241	7.11756e-23
Solanum tuberosum	chr01	5	CH_stu_153	65	161	0.000126983
Solanum tuberosum	chr09	5	CH_stu_35	123	241	4.70797e-22
Solanum tuberosum	chr01	6	CH_stu_129	78	152	0.0000000474866
Solanum tuberosum	chr01	6	CH_stu_117	32	39	0.00000000272722
Thellungiella parvula	ch5-1	5	CH_tpa_30	88	267	0.000378819
Vitis vinifera	chr1	1	CH_vvi_270	19	28	0.000423487
Vitis vinifera	chr1	2	CH_vvi_362	19	28	0.000832102
Vitis vinifera	chr1	4	CH_vvi_100	19	28	0.000423487
Vitis vinifera	chr1	5	CH_vvi_104	19	28	0.000832102
Zea mays	1	1	CH_zma_143	30	62	0.0000503567
Zea mays	1	2	CH_zma_165	30	62	0.000125571
Zea mays	1	4	CH_zma_29	30	62	0.0000503567
Zea mays	1	5	CH_zma_36	30	62	0.000125571

Available child term results

GO term	Description	Number of clusters
GO:0000062	fatty-acyl-CoA binding	1
GO:0000287	magnesium ion binding	8
GO:0005506	iron ion binding	600
GO:0005507	copper ion binding	113
GO:0005509	calcium ion binding	144
GO:0005524	ATP binding	54
GO:0005525	GTP binding	29
GO:0005542	folic acid binding	38
GO:0005543	phospholipid binding	12
GO:0005544	calcium-dependent phospholipid binding	87
GO:0005545	1-phosphatidylinositol binding	1
GO:0005546	phosphatidylinositol-4,5-bisphosphate binding	4
GO:0008198	ferrous iron binding	24
GO:0008199	ferric iron binding	2
GO:0008201	heparin binding	3
GO:0008270	zinc ion binding	175
GO:0008429	phosphatidylethanolamine binding	7
GO:0009374	biotin binding	2
GO:0010013	N-1-naphthylphthalamic acid binding	4
GO:0010181	FMN binding	71
GO:0010427	abscisic acid binding	1
GO:0016151	nickel cation binding	10
GO:0016208	AMP binding	3
GO:0016531	copper chaperone activity	1
GO:0030145	manganese ion binding	274
GO:0030151	molybdenum ion binding	9
GO:0030170	pyridoxal phosphate binding	35
GO:0030553	cGMP binding	3
GO:0030955	potassium ion binding	2
GO:0030976	thiamine pyrophosphate binding	15
GO:0031177	phosphopantetheine binding	3
GO:0031418	L-ascorbic acid binding	11
GO:0032266	phosphatidylinositol-3-phosphate binding	3
GO:0032791	lead ion binding	2
GO:0035091	phosphatidylinositol binding	4
GO:0035639	purine ribonucleoside triphosphate binding	18
GO:0043168	anion binding	34
GO:0043169	cation binding	5
GO:0043295	glutathione binding	9
GO:0043531	ADP binding	1129
GO:0046872	metal ion binding	78
GO:0046914	transition metal ion binding	78
GO:0050660	flavin adenine dinucleotide binding	43
GO:0070401	NADP+ binding	25
GO:0070403	NAD+ binding	6
GO:0080025	phosphatidylinositol-3,5-bisphosphate binding	1
GO:2001227	quercitrin binding	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