PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: InterPro domain
Identifier: IPR001611
Description: Leucine-rich repeat

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00022	13	CH_atr_541	4	5	0.000835208
Amborella trichopoda	scaffold00029	13	CH_atr_146	8	16	0.0000000126044
Amborella trichopoda	scaffold00029	14	CH_atr_38	10	45	0.000000192971
Arabidopsis lyrata	scaffold_8	13	CH_aly_558	9	65	0.000570757
Arabidopsis thaliana	1	13	CH_ath_477	4	4	0.000295895
Arabidopsis thaliana	2	13	CH_ath_420	5	8	0.000155495
Arabidopsis thaliana	5	13	CH_ath_478	4	4	0.000295895
Brassica rapa	A03	13	CH_bra_369	5	7	0.000202959
Brassica rapa	A05	13	CH_bra_274	6	10	0.0000236213
Brassica rapa	A05	14	CH_bra_24	10	58	0.0000713166
Capsella rubella	scaffold_1	13	CH_cru_243	6	7	0.00000103884
Capsella rubella	scaffold_3	13	CH_cru_137	7	7	0.00000000198824
Capsella rubella	scaffold_5	13	CH_cru_103	9	12	0.0000000000734056
Capsella rubella	scaffold_7	13	CH_cru_229	7	11	0.000000626223
Capsella rubella	scaffold_8	13	CH_cru_203	6	6	0.000000150115
Capsella rubella	scaffold_1	14	CH_cru_61	16	208	0.000682185
Capsella rubella	scaffold_5	14	CH_cru_39	10	25	0.0000000123972
Capsella rubella	scaffold_7	14	CH_cru_53	11	74	0.000116265
Citrus sinensis	scaffold00033	13	CH_csi_57	8	8	0.000000000157336
Citrus sinensis	scaffold00152	13	CH_csi_273	5	6	0.000175512
Citrus sinensis	scaffold00305	13	CH_csi_160	7	11	0.00000280947
Citrus sinensis	scaffold00033	14	CH_csi_22	12	86	0.000652857
Citrus sinensis	scaffold00046	14	CH_csi_19	11	59	0.000105721
Cucumis melo	CM3.5_scaffold00005	13	CH_cme_244	7	26	0.0000523939
Cucumis melo	CM3.5_scaffold00060	13	CH_cme_323	4	4	0.000147565
Eucalyptus grandis	scaffold_1	13	CH_egr_346	15	24	0.00000000000183797
Eucalyptus grandis	scaffold_2	13	CH_egr_1316	7	12	0.000977133
Eucalyptus grandis	scaffold_3	13	CH_egr_653	19	75	0.000000103312
Eucalyptus grandis	scaffold_3	13	CH_egr_980	8	13	0.0000519377
Eucalyptus grandis	scaffold_3	13	CH_egr_703	9	12	0.00000030818
Eucalyptus grandis	scaffold_5	13	CH_egr_1288	9	23	0.000824271
Eucalyptus grandis	scaffold_6	13	CH_egr_608	13	28	0.0000000412795
Eucalyptus grandis	scaffold_6	13	CH_egr_115	24	36	6.34582e-23
Eucalyptus grandis	scaffold_7	13	CH_egr_963	6	6	0.0000434924
Eucalyptus grandis	scaffold_1	14	CH_egr_185	15	24	0.00000000000183797
Eucalyptus grandis	scaffold_3	14	CH_egr_224	19	75	0.000000103312
Eucalyptus grandis	scaffold_6	14	CH_egr_221	13	28	0.0000000412795
Eucalyptus grandis	scaffold_7	14	CH_egr_265	10	27	0.000253408
Fragaria vesca	LG3	13	CH_fve_188	10	25	0.00000000921281
Fragaria vesca	LG3	13	CH_fve_259	9	25	0.000000457625
Fragaria vesca	LG3	13	CH_fve_318	8	22	0.00000587658
Fragaria vesca	LG6	13	CH_fve_613	6	14	0.000376862
Fragaria vesca	LG7	13	CH_fve_83	9	10	0.00000000000265365
Fragaria vesca	LG3	14	CH_fve_47	16	123	0.00000016229
Fragaria vesca	LG3	14	CH_fve_32	19	107	0.00000000000420548
Fragaria vesca	LG7	14	CH_fve_52	10	41	0.00000263398
Fragaria vesca	LG7	14	CH_fve_54	16	171	0.000024331
Glycine max	Gm03	13	CH_gma_672	12	80	0.000290954
Glycine max	Gm14	13	CH_gma_260	15	73	0.0000000308133
Glycine max	Gm14	13	CH_gma_532	7	14	0.0000420488
Glycine max	Gm03	14	CH_gma_58	23	200	0.0000000105605
Glycine max	Gm14	14	CH_gma_60	15	73	0.0000000308133
Gossypium raimondii	Chr02	13	CH_gra_194	13	40	0.00000000736001
Gossypium raimondii	Chr07	13	CH_gra_23	24	35	2.12741e-29
Gossypium raimondii	Chr10	13	CH_gra_208	7	7	0.0000000265309
Gossypium raimondii	Chr07	14	CH_gra_1	70	231	6.31106e-60
Gossypium raimondii	Chr10	14	CH_gra_70	13	50	0.00000018319
Gossypium raimondii	Chr11	14	CH_gra_67	29	285	0.00000000525123
Malus domestica	10	13	CH_mdo_145	6	6	0.000000272066
Malus domestica	4	13	CH_mdo_432	7	20	0.000244042
Malus domestica	8	13	CH_mdo_592	10	65	0.000816512
Malus domestica	8	14	CH_mdo_38	10	65	0.000816512
Manihot esculenta	scaffold08686	13	CH_mes_86	7	9	0.0000000410114
Manihot esculenta	scaffold08686	14	CH_mes_11	10	30	0.000000054828
Medicago truncatula	chr2	13	CH_mtr_1017	6	12	0.000216425
Medicago truncatula	chr3	13	CH_mtr_247	11	21	0.0000000000232873
Medicago truncatula	chr4	13	CH_mtr_1206	9	50	0.000760748
Medicago truncatula	chr4	13	CH_mtr_97	21	79	2.2326e-17
Medicago truncatula	chr6	13	CH_mtr_291	12	33	0.000000000255437
Medicago truncatula	chr7	13	CH_mtr_283	14	52	0.000000000159388
Medicago truncatula	chr8	13	CH_mtr_223	17	76	0.00000000000501966
Medicago truncatula	chr3	14	CH_mtr_122	11	21	0.0000000000232873
Medicago truncatula	chr6	14	CH_mtr_127	12	33	0.000000000255437
Oryza sativa ssp. japonica	1	13	CH_osa_791	6	20	0.000553257
Oryza sativa ssp. japonica	11	13	CH_osa_38	15	22	3.25988e-22
Oryza sativa ssp. japonica	2	13	CH_osa_9	24	39	4.83129e-36
Oryza sativa ssp. japonica	11	14	CH_osa_36	15	22	3.25988e-22
Oryza sativa ssp. japonica	2	14	CH_osa_100	17	205	0.0000000871033
Oryza sativa ssp. japonica	2	14	CH_osa_10	24	39	4.83129e-36
Physcomitrella patens	scaffold_107	13	CH_ppa_4	8	8	0.0000000000016068
Physcomitrella patens	scaffold_2	13	CH_ppa_10	6	6	0.0000000192275
Physcomitrella patens	scaffold_107	14	CH_ppa_1	11	27	0.000000000013638
Populus trichocarpa	Chr03	13	CH_ptr_281	13	44	0.0000000329802
Populus trichocarpa	Chr04	13	CH_ptr_337	8	12	0.00000024621
Populus trichocarpa	Chr05	13	CH_ptr_330	9	17	0.000000206968
Populus trichocarpa	Chr05	13	CH_ptr_222	17	77	0.00000000203708
Populus trichocarpa	Chr11	13	CH_ptr_633	12	69	0.000198637
Populus trichocarpa	Chr18	13	CH_ptr_376	8	13	0.000000629722
Populus trichocarpa	scaffold_24	13	CH_ptr_427	9	22	0.00000389778
Populus trichocarpa	Chr03	14	CH_ptr_92	13	44	0.0000000329802
Populus trichocarpa	Chr05	14	CH_ptr_82	22	103	0.00000000000084254
Populus trichocarpa	Chr11	14	CH_ptr_104	10	38	0.0000525949
Populus trichocarpa	Chr15	14	CH_ptr_98	10	26	0.000000722248
Populus trichocarpa	Chr18	14	CH_ptr_101	11	43	0.0000108852
Prunus persica	scaffold_2	13	CH_ppe_259	12	31	0.0000000237883
Prunus persica	scaffold_4	13	CH_ppe_47	17	22	2.3974e-20
Prunus persica	scaffold_4	13	CH_ppe_704	6	10	0.00052395
Prunus persica	scaffold_2	14	CH_ppe_87	12	31	0.0000000237883
Prunus persica	scaffold_4	14	CH_ppe_42	31	120	2.19123e-20
Ricinus communis	29929	13	CH_rco_267	5	7	0.0000973068
Solanum lycopersicum	ch01	13	CH_sly_649	7	25	0.000325103
Solanum lycopersicum	ch01	13	CH_sly_695	5	8	0.000350105
Solanum lycopersicum	ch02	13	CH_sly_254	13	73	0.0000000699265
Solanum lycopersicum	ch02	14	CH_sly_61	14	90	0.0000000681735
Solanum lycopersicum	ch12	14	CH_sly_58	11	37	0.00000000809034
Solanum tuberosum	chr01	13	CH_stu_404	10	21	0.0000000215458
Solanum tuberosum	chr01	13	CH_stu_373	8	10	0.000000011036
Solanum tuberosum	chr01	13	CH_stu_1082	9	40	0.000727971
Solanum tuberosum	chr04	13	CH_stu_227	18	70	0.0000000000046263
Solanum tuberosum	chr05	13	CH_stu_383	7	7	0.000000014899
Solanum tuberosum	chr07	13	CH_stu_644	7	12	0.0000109484
Solanum tuberosum	chr08	13	CH_stu_495	7	9	0.000000520528
Solanum tuberosum	chr12	13	CH_stu_68	21	38	4.60897e-23
Solanum tuberosum	chr01	14	CH_stu_125	10	21	0.0000000215458
Solanum tuberosum	chr08	14	CH_stu_146	13	86	0.0000958498
Solanum tuberosum	chr12	14	CH_stu_63	21	38	4.60897e-23
Theobroma cacao	scaffold_10r	13	CH_tca_398	13	77	0.0000196547
Theobroma cacao	scaffold_2	13	CH_tca_548	5	6	0.00023976
Theobroma cacao	scaffold_4	13	CH_tca_646	5	7	0.000827384
Theobroma cacao	scaffold_7	13	CH_tca_19	21	28	1.36771e-27
Theobroma cacao	scaffold_7	13	CH_tca_288	6	6	0.000000681149
Theobroma cacao	scaffold_7	13	CH_tca_21	29	79	9.0952e-27
Theobroma cacao	scaffold_7	13	CH_tca_396	7	13	0.0000179411
Theobroma cacao	scaffold_8	13	CH_tca_272	10	27	0.000000346666
Theobroma cacao	scaffold_10r	14	CH_tca_61	21	229	0.0000135291
Theobroma cacao	scaffold_7	14	CH_tca_19	21	28	1.36771e-27
Theobroma cacao	scaffold_7	14	CH_tca_8	50	176	3.00136e-42
Theobroma cacao	scaffold_8	14	CH_tca_54	10	27	0.000000346666
Vitis vinifera	chr12	13	CH_vvi_421	9	27	0.0000260989
Vitis vinifera	chr16	13	CH_vvi_569	9	34	0.000259638
Vitis vinifera	chr18	13	CH_vvi_293	11	34	0.00000049977
Vitis vinifera	chr18	13	CH_vvi_426	6	8	0.0000316761
Vitis vinifera	chr18	13	CH_vvi_387	14	79	0.00000655433
Vitis vinifera	chr5	13	CH_vvi_498	6	9	0.000093506
Vitis vinifera	chr16	14	CH_vvi_91	17	162	0.000344047
Vitis vinifera	chr18	14	CH_vvi_55	35	295	0.000000000000132582
Zea mays	10	13	CH_zma_173	5	5	0.000000606338

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