PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0055085
Description: transmembrane transport

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00038	1	CH_atr_138	6	8	0.0000381661
Amborella trichopoda	scaffold00041	1	CH_atr_187	6	10	0.000276787
Amborella trichopoda	scaffold00154	1	CH_atr_195	5	6	0.000427891
Amborella trichopoda	scaffold00019	2	CH_atr_236	5	6	0.000777254
Amborella trichopoda	scaffold00032	2	CH_atr_148	6	8	0.0000780307
Amborella trichopoda	scaffold00038	2	CH_atr_149	6	8	0.0000780307
Amborella trichopoda	scaffold00154	2	CH_atr_235	5	6	0.000777254
Amborella trichopoda	scaffold00013	3	CH_atr_303	5	5	0.000341815
Amborella trichopoda	scaffold00038	3	CH_atr_292	6	8	0.00024276
Beta vulgaris	0033.scaffold00127	2	CH_bvu_79	9	12	0.0000000562265
Capsella rubella	scaffold_3	1	CH_cru_123	6	6	0.0000069709
Capsella rubella	scaffold_3	2	CH_cru_176	6	6	0.0000125074
Citrullus lanatus	Chr2	2	CH_cla_53	9	10	0.000000000844999
Citrus sinensis	scaffold00013	1	CH_csi_86	6	6	0.0000111306
Cucumis melo	CM3.5_scaffold00017	2	CH_cme_95	8	13	0.00000139102
Cucumis melo	CM3.5_scaffold00011	6	CH_cme_35	10	20	0.000000539399
Eucalyptus grandis	scaffold_11	1	CH_egr_429	6	6	0.0000130316
Eucalyptus grandis	scaffold_3	1	CH_egr_595	5	5	0.000485344
Eucalyptus grandis	scaffold_7	1	CH_egr_596	5	5	0.000485344
Eucalyptus grandis	scaffold_9	1	CH_egr_594	5	5	0.000485344
Eucalyptus grandis	scaffold_11	2	CH_egr_445	7	7	0.000000608882
Eucalyptus grandis	scaffold_11	2	CH_egr_547	6	6	0.0000209654
Eucalyptus grandis	scaffold_11	3	CH_egr_652	6	6	0.0000468379
Fragaria vesca	LG6	2	CH_fve_50	11	18	0.000000000240049
Fragaria vesca	LG6	3	CH_fve_95	11	18	0.00000000349604
Fragaria vesca	LG4	4	CH_fve_51	10	44	0.000208754
Fragaria vesca	LG4	5	CH_fve_71	10	44	0.000559447
Fragaria vesca	LG6	5	CH_fve_15	11	18	0.000000000240049
Fragaria vesca	LG6	6	CH_fve_34	11	18	0.00000000349604
Fragaria vesca	LG7	6	CH_fve_29	35	262	0.000000000114925
Gossypium raimondii	Chr11	1	CH_gra_263	5	5	0.000519658
Gossypium raimondii	Chr02	2	CH_gra_348	5	5	0.000787359
Gossypium raimondii	Chr07	2	CH_gra_110	9	11	0.0000000291693
Gossypium raimondii	Chr11	2	CH_gra_347	5	5	0.000787359
Malus domestica	7	2	CH_mdo_19	10	16	0.00000000104862
Malus domestica	7	3	CH_mdo_64	10	16	0.0000000171453
Malus domestica	7	5	CH_mdo_6	10	16	0.00000000104862
Malus domestica	1	6	CH_mdo_11	32	239	0.000000000139731
Malus domestica	7	6	CH_mdo_18	24	164	0.0000000615391
Malus domestica	7	6	CH_mdo_15	10	16	0.0000000171453
Manihot esculenta	scaffold03604	1	CH_mes_150	6	9	0.00049304
Manihot esculenta	scaffold03604	2	CH_mes_230	6	9	0.000863682
Manihot esculenta	scaffold03604	3	CH_mes_145	7	9	0.0000298016
Manihot esculenta	scaffold03604	6	CH_mes_26	10	30	0.000503632
Medicago truncatula	chr6	4	CH_mtr_137	13	86	0.00000614124
Medicago truncatula	chr6	5	CH_mtr_156	13	86	0.0000180217
Medicago truncatula	chr6	6	CH_mtr_242	13	86	0.000261191
Oryza sativa ssp. japonica	9	1	CH_osa_228	5	5	0.0000178981
Oryza sativa ssp. japonica	9	2	CH_osa_236	5	5	0.0000281458
Oryza sativa ssp. japonica	11	3	CH_osa_441	7	18	0.000417294
Oryza sativa ssp. japonica	9	3	CH_osa_323	5	5	0.0000598305
Populus trichocarpa	Chr17	2	CH_ptr_275	8	14	0.0000308224
Prunus persica	scaffold_4	2	CH_ppe_363	6	8	0.000347699
Prunus persica	scaffold_4	3	CH_ppe_497	6	8	0.000620063
Prunus persica	scaffold_2	6	CH_ppe_154	22	174	0.000627499
Solanum lycopersicum	ch05	6	CH_sly_125	10	26	0.000036588
Solanum tuberosum	chr05	1	CH_stu_426	5	5	0.000209857
Solanum tuberosum	chr03	3	CH_stu_651	6	7	0.000215413
Solanum tuberosum	chr03	4	CH_stu_97	10	19	0.0000000932689
Solanum tuberosum	chr03	5	CH_stu_90	11	19	0.00000000441629
Solanum tuberosum	chr03	6	CH_stu_130	11	19	0.0000000536804
Solanum tuberosum	chr05	6	CH_stu_222	11	38	0.000496225
Thellungiella parvula	ch3-1	2	CH_tpa_174	5	5	0.000317003
Theobroma cacao	scaffold_10r	1	CH_tca_217	7	12	0.0000667256
Theobroma cacao	scaffold_10r	2	CH_tca_257	7	12	0.000116233
Theobroma cacao	scaffold_10r	3	CH_tca_370	7	12	0.000245348
Vitis vinifera	chr4	1	CH_vvi_180	6	6	0.00000500253
Vitis vinifera	chr14	2	CH_vvi_39	13	14	9.14018e-16
Vitis vinifera	chr4	2	CH_vvi_209	6	6	0.00000851497
Vitis vinifera	chr13	3	CH_vvi_400	7	11	0.0002505
Vitis vinifera	chr4	3	CH_vvi_212	7	7	0.000000849014
Vitis vinifera	chr14	5	CH_vvi_29	13	14	9.14018e-16
Vitis vinifera	chr19	5	CH_vvi_56	12	28	0.0000000535956
Vitis vinifera	chr19	6	CH_vvi_66	14	28	0.000000000678622
Zea mays	7	1	CH_zma_157	5	5	0.0000948927
Zea mays	7	2	CH_zma_171	5	5	0.000149157

Available child term results

GO term	Description	Number of clusters
GO:0003333	amino acid transmembrane transport	22
GO:0006855	drug transmembrane transport	187
GO:0010107	potassium ion import	1
GO:0015986	ATP synthesis coupled proton transport	7
GO:0016558	protein import into peroxisome matrix	1
GO:0031204	posttranslational protein targeting to membrane, translocation	4
GO:0034220	ion transmembrane transport	2
GO:0034755	iron ion transmembrane transport	8
GO:0034775	glutathione transmembrane transport	6
GO:0035434	copper ion transmembrane transport	30
GO:0035436	triose phosphate transmembrane transport	2
GO:0035674	tricarboxylic acid transmembrane transport	2
GO:0035725	sodium ion transmembrane transport	8
GO:0045037	protein import into chloroplast stroma	3
GO:0045039	protein import into mitochondrial inner membrane	5
GO:0045040	protein import into mitochondrial outer membrane	9
GO:0070588	calcium ion transmembrane transport	7
GO:0071423	malate transmembrane transport	4
GO:0071435	potassium ion export	14
GO:0071577	zinc ion transmembrane transport	23
GO:0071805	potassium ion transmembrane transport	41
GO:0072488	ammonium transmembrane transport	2
GO:0080170	hydrogen peroxide transmembrane transport	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