PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0016023
Description: cytoplasmic membrane-bounded vesicle

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00041	3	CH_atr_2	25	29	1.94154e-56
Amborella trichopoda	scaffold00134	3	CH_atr_77	6	9	0.00000000160865
Amborella trichopoda	scaffold00041	6	CH_atr_4	25	29	1.94154e-56
Arabidopsis lyrata	scaffold_3	3	CH_aly_394	3	3	0.000854375
Arabidopsis lyrata	scaffold_7	3	CH_aly_395	3	3	0.000854375
Beta vulgaris	0008.scaffold00029	3	CH_bvu_156	4	4	0.00000449463
Beta vulgaris	Bvchr3.sca003	3	CH_bvu_213	4	6	0.0000670124
Beta vulgaris	Bvchr6.sca002	3	CH_bvu_155	5	10	0.00000414639
Beta vulgaris	Bvchr9.sca025	3	CH_bvu_85	5	5	0.0000000167119
Carica papaya	supercontig_85	3	CH_cpa_29	6	6	0.0000000000160353
Carica papaya	supercontig_9	3	CH_cpa_328	3	3	0.000617559
Citrullus lanatus	Chr11	3	CH_cla_127	4	4	0.00000190327
Citrus sinensis	scaffold00038	3	CH_csi_57	5	5	0.000000024937
Citrus sinensis	scaffold00043	3	CH_csi_179	5	17	0.000147981
Cucumis melo	CM3.5_scaffold00008	3	CH_cme_318	3	3	0.000546661
Cucumis melo	CM3.5_scaffold00022	3	CH_cme_149	4	4	0.00000146468
Eucalyptus grandis	scaffold_1	3	CH_egr_78	10	10	1.0815e-21
Eucalyptus grandis	scaffold_1	3	CH_egr_868	3	3	0.000853356
Eucalyptus grandis	scaffold_8	3	CH_egr_869	3	3	0.000853356
Eucalyptus grandis	scaffold_9	3	CH_egr_556	4	4	0.00000244322
Eucalyptus grandis	scaffold_1	6	CH_egr_67	10	10	1.0815e-21
Fragaria vesca	LG1	3	CH_fve_392	3	3	0.000531215
Fragaria vesca	LG2	3	CH_fve_132	5	7	0.0000000661566
Fragaria vesca	LG3	3	CH_fve_54	6	6	0.00000000000757701
Fragaria vesca	LG4	3	CH_fve_172	5	10	0.000000789064
Glycine max	Gm01	3	CH_gma_305	5	11	0.0000128262
Glycine max	Gm03	3	CH_gma_151	5	5	0.0000000282478
Glycine max	Gm03	3	CH_gma_78	7	9	0.0000000000119064
Glycine max	Gm16	3	CH_gma_149	5	5	0.0000000282478
Glycine max	Gm19	3	CH_gma_179	5	6	0.000000168998
Glycine max	Gm19	3	CH_gma_150	5	5	0.0000000282478
Gossypium raimondii	Chr01	3	CH_gra_217	4	4	0.0000189247
Gossypium raimondii	Chr02	3	CH_gra_149	5	5	0.0000000884806
Gossypium raimondii	Chr02	3	CH_gra_176	5	7	0.00000184363
Gossypium raimondii	Chr04	3	CH_gra_104	6	6	0.000000000411329
Gossypium raimondii	Chr09	3	CH_gra_36	9	9	3.99213e-17
Gossypium raimondii	Chr09	6	CH_gra_31	10	14	1.78539e-16
Lotus japonicus	chr1	3	CH_lja_138	3	3	0.000141181
Medicago truncatula	chr4	3	CH_mtr_50	10	18	3.80639e-19
Medicago truncatula	chr7	3	CH_mtr_320	5	9	0.000000106709
Medicago truncatula	chr7	3	CH_mtr_580	5	26	0.0000544255
Medicago truncatula	chr4	6	CH_mtr_48	10	18	3.80639e-19
Oryza sativa ssp. japonica	10	1	CH_osa_300	18	46	0.000152477
Oryza sativa ssp. japonica	10	1	CH_osa_59	24	40	0.00000000000160115
Oryza sativa ssp. japonica	2	1	CH_osa_276	8	8	0.0000654773
Oryza sativa ssp. japonica	7	1	CH_osa_369	8	9	0.000549272
Oryza sativa ssp. japonica	8	1	CH_osa_372	19	55	0.000632551
Oryza sativa ssp. japonica	10	2	CH_osa_321	18	46	0.000159973
Oryza sativa ssp. japonica	10	2	CH_osa_57	24	40	0.00000000000171551
Oryza sativa ssp. japonica	2	2	CH_osa_277	8	8	0.0000670833
Oryza sativa ssp. japonica	7	2	CH_osa_391	8	9	0.00056262
Oryza sativa ssp. japonica	8	2	CH_osa_402	19	55	0.000664408
Oryza sativa ssp. japonica	1	3	CH_osa_218	11	13	0.00000259686
Oryza sativa ssp. japonica	10	3	CH_osa_409	15	32	0.000225595
Oryza sativa ssp. japonica	10	3	CH_osa_68	24	40	0.00000000000286559
Oryza sativa ssp. japonica	11	3	CH_osa_488	21	66	0.000915142
Oryza sativa ssp. japonica	2	3	CH_osa_337	8	8	0.0000803406
Oryza sativa ssp. japonica	7	3	CH_osa_468	8	9	0.000672684
Oryza sativa ssp. japonica	8	3	CH_osa_377	20	55	0.000144322
Oryza sativa ssp. japonica	9	3	CH_osa_139	17	27	0.0000000348328
Oryza sativa ssp. japonica	1	4	CH_osa_62	54	238	0.0000000208248
Oryza sativa ssp. japonica	10	4	CH_osa_42	24	40	0.00000000000160115
Oryza sativa ssp. japonica	10	4	CH_osa_131	18	46	0.000152477
Oryza sativa ssp. japonica	11	4	CH_osa_51	36	104	0.00000000019479
Oryza sativa ssp. japonica	2	4	CH_osa_167	14	31	0.00098263
Oryza sativa ssp. japonica	8	4	CH_osa_157	19	55	0.000632551
Oryza sativa ssp. japonica	1	5	CH_osa_69	54	238	0.0000000234652
Oryza sativa ssp. japonica	10	5	CH_osa_44	24	40	0.00000000000171551
Oryza sativa ssp. japonica	10	5	CH_osa_149	18	46	0.000159973
Oryza sativa ssp. japonica	11	5	CH_osa_52	36	104	0.00000000021375
Oryza sativa ssp. japonica	8	5	CH_osa_170	19	55	0.000664408
Oryza sativa ssp. japonica	1	6	CH_osa_114	11	13	0.00000259686
Oryza sativa ssp. japonica	10	6	CH_osa_56	24	40	0.00000000000286559
Oryza sativa ssp. japonica	10	6	CH_osa_158	15	32	0.000225595
Oryza sativa ssp. japonica	11	6	CH_osa_95	48	206	0.000000364437
Oryza sativa ssp. japonica	11	6	CH_osa_65	36	104	0.000000000425975
Oryza sativa ssp. japonica	8	6	CH_osa_154	20	55	0.000144322
Oryza sativa ssp. japonica	9	6	CH_osa_88	17	27	0.0000000348328
Oryza sativa ssp. japonica	10	7	CH_osa_25	11	21	0.0000184716
Oryza sativa ssp. japonica	10	8	CH_osa_23	11	21	0.0000194155
Oryza sativa ssp. japonica	10	9	CH_osa_25	11	21	0.0000218786
Oryza sativa ssp. japonica	10	10	CH_osa_35	11	21	0.0000184716
Oryza sativa ssp. japonica	10	11	CH_osa_44	11	21	0.0000194155
Oryza sativa ssp. japonica	10	12	CH_osa_49	11	21	0.0000218786
Populus trichocarpa	Chr01	3	CH_ptr_301	4	4	0.00000407998
Populus trichocarpa	Chr16	3	CH_ptr_300	4	4	0.00000407998
Populus trichocarpa	Chr17	3	CH_ptr_193	5	5	0.0000000127004
Prunus persica	scaffold_2	3	CH_ppe_527	3	3	0.000826195
Prunus persica	scaffold_3	3	CH_ppe_252	4	4	0.00000250155
Prunus persica	scaffold_3	3	CH_ppe_320	4	6	0.0000373411
Prunus persica	scaffold_6	3	CH_ppe_253	4	4	0.00000250155
Prunus persica	scaffold_8	3	CH_ppe_296	5	14	0.0000146499
Prunus persica	scaffold_8	3	CH_ppe_528	3	3	0.000826195
Ricinus communis	29986	3	CH_rco_296	3	3	0.000791814
Ricinus communis	30190	3	CH_rco_146	4	4	0.00000260504
Solanum lycopersicum	ch02	3	CH_sly_620	3	3	0.00075102
Solanum lycopersicum	ch09	3	CH_sly_369	4	6	0.0000305686
Solanum lycopersicum	ch10	3	CH_sly_216	7	33	0.000000156379
Solanum tuberosum	chr02	3	CH_stu_747	3	3	0.00059065
Solanum tuberosum	chr09	3	CH_stu_748	3	3	0.00059065
Theobroma cacao	scaffold_1	3	CH_tca_450	3	3	0.00090462
Theobroma cacao	scaffold_2	3	CH_tca_15	11	12	6.17496e-23
Theobroma cacao	scaffold_4	3	CH_tca_120	5	5	0.00000000841999
Theobroma cacao	scaffold_5	3	CH_tca_218	5	10	0.00000209509
Theobroma cacao	scaffold_2	6	CH_tca_16	11	12	6.17496e-23
Vitis vinifera	chr12	3	CH_vvi_415	3	3	0.000388286
Vitis vinifera	chr14	3	CH_vvi_214	4	4	0.00000091997
Vitis vinifera	chr6	3	CH_vvi_280	4	6	0.0000137471
Vitis vinifera	chr8	3	CH_vvi_281	4	6	0.0000137471
Zea mays	2	3	CH_zma_106	9	74	0.00000107513
Zea mays	2	6	CH_zma_25	10	85	0.000000115844

Available child term results

GO term	Description	Number of clusters
GO:0012507	ER to Golgi transport vesicle membrane	1
GO:0030126	COPI vesicle coat	11
GO:0030127	COPII vesicle coat	2
GO:0030130	clathrin coat of trans-Golgi network vesicle	1
GO:0030134	ER to Golgi transport vesicle	3
GO:0030659	cytoplasmic vesicle membrane	2
GO:0030665	clathrin-coated vesicle membrane	2
GO:0033095	aleurone grain	6
GO:0043660	bacteroid-containing symbiosome	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