PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0030001
Description: metal ion transport

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_8	1	CH_aly_93	5	5	0.000000500359
Arabidopsis lyrata	scaffold_8	2	CH_aly_154	5	5	0.00000241373
Arabidopsis lyrata	scaffold_8	3	CH_aly_183	5	5	0.00000349219
Arabidopsis lyrata	scaffold_8	6	CH_aly_89	10	81	0.00035083
Cucumis melo	CM3.5_scaffold00005	1	CH_cme_108	4	4	0.000037204
Cucumis melo	CM3.5_scaffold00005	2	CH_cme_166	4	4	0.000114325
Cucumis melo	CM3.5_scaffold00005	3	CH_cme_258	4	4	0.000169544
Cucumis melo	CM3.5_scaffold00035	3	CH_cme_170	5	6	0.00000896679
Eucalyptus grandis	scaffold_1	1	CH_egr_278	6	6	0.0000000190704
Eucalyptus grandis	scaffold_5	1	CH_egr_159	9	12	0.00000000000292695
Eucalyptus grandis	scaffold_8	1	CH_egr_568	6	18	0.000322615
Eucalyptus grandis	scaffold_1	2	CH_egr_385	6	6	0.0000000826921
Eucalyptus grandis	scaffold_5	2	CH_egr_161	10	11	0.0000000000000154136
Eucalyptus grandis	scaffold_1	3	CH_egr_859	5	8	0.000673792
Eucalyptus grandis	scaffold_1	3	CH_egr_453	6	6	0.000000159768
Eucalyptus grandis	scaffold_11	3	CH_egr_326	12	34	0.000000000291075
Eucalyptus grandis	scaffold_5	3	CH_egr_35	17	17	2.18037e-28
Eucalyptus grandis	scaffold_5	3	CH_egr_213	13	29	0.000000000000488822
Eucalyptus grandis	scaffold_5	4	CH_egr_56	21	85	6.79606e-20
Eucalyptus grandis	scaffold_11	6	CH_egr_166	12	34	0.000000000291075
Eucalyptus grandis	scaffold_5	6	CH_egr_36	17	17	2.18037e-28
Fragaria vesca	LG2	1	CH_fve_123	5	7	0.00000307332
Fragaria vesca	LG3	1	CH_fve_100	6	12	0.000000699694
Fragaria vesca	LG2	2	CH_fve_156	5	7	0.0000117018
Fragaria vesca	LG3	2	CH_fve_139	6	12	0.00000347659
Fragaria vesca	LG2	3	CH_fve_234	5	7	0.0000243345
Fragaria vesca	LG3	3	CH_fve_206	5	6	0.00000699973
Fragaria vesca	LG3	3	CH_fve_212	6	12	0.00000835535
Fragaria vesca	LG3	6	CH_fve_96	10	98	0.000279744
Glycine max	Gm09	1	CH_gma_128	7	12	0.000000190017
Glycine max	Gm16	1	CH_gma_63	7	7	0.000000000249485
Glycine max	Gm09	2	CH_gma_181	7	12	0.000000907547
Glycine max	Gm16	2	CH_gma_92	7	7	0.0000000012035
Glycine max	Gm09	3	CH_gma_245	7	12	0.0000017307
Glycine max	Gm16	3	CH_gma_123	7	7	0.00000000230617
Gossypium raimondii	Chr09	3	CH_gra_409	4	4	0.000751028
Manihot esculenta	scaffold08316	2	CH_mes_227	9	74	0.00071121
Manihot esculenta	scaffold08316	2	CH_mes_149	4	4	0.000165943
Manihot esculenta	scaffold08316	3	CH_mes_208	4	4	0.000266706
Medicago truncatula	chr3	6	CH_mtr_276	11	173	0.00092491
Oryza sativa ssp. japonica	2	1	CH_osa_157	5	6	0.000000357202
Oryza sativa ssp. japonica	2	2	CH_osa_161	5	6	0.000000603374
Oryza sativa ssp. japonica	2	3	CH_osa_162	7	18	0.000000185342
Oryza sativa ssp. japonica	4	3	CH_osa_74	7	7	0.00000000000612318
Oryza sativa ssp. japonica	4	3	CH_osa_142	7	15	0.0000000379927
Physcomitrella patens	scaffold_57	1	CH_ppa_5	7	7	0.0000000000277095
Physcomitrella patens	scaffold_57	2	CH_ppa_5	7	7	0.000000000073193
Physcomitrella patens	scaffold_57	3	CH_ppa_9	7	7	0.000000000225115
Populus trichocarpa	Chr06	1	CH_ptr_18	16	22	1.53754e-24
Populus trichocarpa	Chr17	1	CH_ptr_223	5	6	0.0000104088
Populus trichocarpa	Chr17	2	CH_ptr_269	5	6	0.0000274853
Populus trichocarpa	Chr17	3	CH_ptr_211	7	9	0.0000000395475
Populus trichocarpa	Chr06	4	CH_ptr_17	16	22	1.53754e-24
Prunus persica	scaffold_6	1	CH_ppe_193	5	6	0.00000346977
Prunus persica	scaffold_6	2	CH_ppe_244	5	6	0.0000160854
Prunus persica	scaffold_6	3	CH_ppe_171	6	6	0.0000000405074
Prunus persica	scaffold_6	6	CH_ppe_156	15	225	0.000682574
Solanum lycopersicum	ch07	3	CH_sly_500	4	4	0.000211087
Thellungiella parvula	ch6-6	1	CH_tpa_76	5	7	0.0000173749
Thellungiella parvula	ch6-6	2	CH_tpa_116	5	7	0.0000779732
Thellungiella parvula	ch6-6	3	CH_tpa_163	5	7	0.000114712
Theobroma cacao	scaffold_6	1	CH_tca_181	6	13	0.00000716152
Theobroma cacao	scaffold_7	1	CH_tca_141	6	10	0.000000892828
Theobroma cacao	scaffold_6	2	CH_tca_222	6	13	0.0000305897
Theobroma cacao	scaffold_7	2	CH_tca_181	6	10	0.00000383351
Theobroma cacao	scaffold_6	3	CH_tca_183	7	13	0.000000462592
Theobroma cacao	scaffold_7	3	CH_tca_379	4	4	0.000293882
Theobroma cacao	scaffold_7	3	CH_tca_240	6	10	0.00000584974
Theobroma cacao	scaffold_7	4	CH_tca_66	13	203	0.000119605
Theobroma cacao	scaffold_7	5	CH_tca_83	11	121	0.00060298
Theobroma cacao	scaffold_7	6	CH_tca_100	12	121	0.0001102
Vitis vinifera	chr16	1	CH_vvi_177	5	6	0.00000362942
Vitis vinifera	chrUn	1	CH_vvi_115	6	7	0.0000000310506
Vitis vinifera	chr16	2	CH_vvi_216	5	6	0.0000123419
Vitis vinifera	chrUn	2	CH_vvi_142	6	7	0.000000135362
Vitis vinifera	chr12_random	3	CH_vvi_257	5	5	0.0000054546
Vitis vinifera	chr16	3	CH_vvi_170	6	6	0.0000000623664
Vitis vinifera	chrUn	3	CH_vvi_197	6	7	0.000000432284
Zea mays	2	3	CH_zma_38	8	10	0.0000000000599185
Zea mays	5	3	CH_zma_254	5	9	0.000253354

Available child term results

GO term	Description	Number of clusters
GO:0006814	sodium ion transport	1
GO:0006816	calcium ion transport	1
GO:0006826	iron ion transport	5
GO:0006829	zinc ion transport	1
GO:0010107	potassium ion import	1
GO:0010351	lithium ion transport	4
GO:0015684	ferrous iron transport	2
GO:0015690	aluminum cation transport	2
GO:0015692	lead ion transport	4
GO:0034755	iron ion transmembrane transport	8
GO:0034756	regulation of iron ion transport	2
GO:0035434	copper ion transmembrane transport	30
GO:0035725	sodium ion transmembrane transport	8
GO:0043268	positive regulation of potassium ion transport	4
GO:0051928	positive regulation of calcium ion transport	3
GO:0070588	calcium ion transmembrane transport	7
GO:0070838	divalent metal ion transport	4
GO:0071435	potassium ion export	14
GO:0071577	zinc ion transmembrane transport	23
GO:0071805	potassium ion transmembrane transport	41

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