PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: Mapman term
Identifier: 26.8
Description: misc.nitrilases, *nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_1	17	CH_aly_50	4	7	0.0000128321
Arabidopsis lyrata	scaffold_4	17	CH_aly_29	4	4	0.000000368227
Arabidopsis lyrata	scaffold_4	17	CH_aly_16	5	6	0.0000000039004
Arabidopsis lyrata	scaffold_7	17	CH_aly_51	4	7	0.0000128321
Arabidopsis lyrata	scaffold_8	17	CH_aly_21	5	8	0.0000000362961
Arabidopsis thaliana	1	17	CH_ath_120	5	5	0.00000000162489
Arabidopsis thaliana	1	17	CH_ath_106	6	9	0.000000000282848
Arabidopsis thaliana	2	17	CH_ath_68	7	8	0.0000000000000555219
Arabidopsis thaliana	2	17	CH_ath_12	14	25	3.07753e-27
Arabidopsis thaliana	4	17	CH_ath_153	5	7	0.0000000340023
Arabidopsis thaliana	5	17	CH_ath_133	6	14	0.0000000100216
Arabidopsis thaliana	2	18	CH_ath_23	14	25	3.07753e-27
Brassica rapa	A01	17	CH_bra_87	5	7	0.000000308273
Brassica rapa	A04	17	CH_bra_14	8	12	0.000000000000227723
Brassica rapa	A04	17	CH_bra_88	5	7	0.000000308273
Brassica rapa	A05	17	CH_bra_10	9	15	0.00000000000000711905
Brassica rapa	A09	17	CH_bra_36	6	8	0.00000000130848
Brassica rapa	A09	17	CH_bra_53	6	10	0.00000000976004
Brassica rapa	A05	18	CH_bra_20	10	105	0.0000000985587
Capsella rubella	scaffold_1	17	CH_cru_130	5	6	0.000000098145
Capsella rubella	scaffold_1	17	CH_cru_48	7	9	0.00000000000715985
Capsella rubella	scaffold_4	17	CH_cru_7	14	20	3.38935e-26
Capsella rubella	scaffold_4	17	CH_cru_29	8	8	6.87423e-16
Capsella rubella	scaffold_7	17	CH_cru_49	7	9	0.00000000000715985
Capsella rubella	scaffold_8	17	CH_cru_131	5	6	0.000000098145
Capsella rubella	scaffold_4	18	CH_cru_7	14	20	3.38935e-26
Citrus sinensis	scaffold00008	17	CH_csi_26	6	6	0.0000000000271359
Citrus sinensis	scaffold00010	17	CH_csi_12	8	9	0.0000000000000024671
Citrus sinensis	scaffold00026	17	CH_csi_98	4	4	0.00000249297
Citrus sinensis	scaffold00159	17	CH_csi_99	4	4	0.00000249297
Citrus sinensis	scaffold00163	17	CH_csi_67	5	7	0.000000173284
Eucalyptus grandis	scaffold_10	17	CH_egr_78	11	13	6.87408e-22
Eucalyptus grandis	scaffold_4	17	CH_egr_320	6	8	0.000000000983009
Eucalyptus grandis	scaffold_4	17	CH_egr_36	14	15	3.24258e-30
Eucalyptus grandis	scaffold_4	17	CH_egr_186	8	11	0.0000000000000542201
Eucalyptus grandis	scaffold_8	17	CH_egr_97	10	11	3.28238e-20
Eucalyptus grandis	scaffold_9	17	CH_egr_86	10	10	2.99213e-21
Eucalyptus grandis	scaffold_9	17	CH_egr_369	7	19	0.0000000053002
Eucalyptus grandis	scaffold_9	17	CH_egr_112	11	19	6.55312e-19
Eucalyptus grandis	scaffold_10	18	CH_egr_71	11	13	6.87408e-22
Eucalyptus grandis	scaffold_4	18	CH_egr_38	14	15	3.24258e-30
Eucalyptus grandis	scaffold_8	18	CH_egr_83	10	11	3.28238e-20
Eucalyptus grandis	scaffold_9	18	CH_egr_77	10	10	2.99213e-21
Eucalyptus grandis	scaffold_9	18	CH_egr_95	11	19	6.55312e-19
Glycine max	Gm02	17	CH_gma_39	8	8	1.02011e-16
Glycine max	Gm04	17	CH_gma_244	4	4	0.0000024846
Glycine max	Gm05	17	CH_gma_40	9	13	1.79645e-16
Glycine max	Gm08	17	CH_gma_28	9	10	2.52947e-18
Glycine max	Gm09	17	CH_gma_47	9	17	0.00000000000000605343
Glycine max	Gm11	17	CH_gma_242	4	4	0.0000024846
Glycine max	Gm12	17	CH_gma_243	4	4	0.0000024846
Glycine max	Gm15	17	CH_gma_53	9	19	0.0000000000000229002
Glycine max	Gm18	17	CH_gma_346	4	7	0.000086423
Glycine max	Gm05	18	CH_gma_33	10	39	0.000000000000372478
Glycine max	Gm08	18	CH_gma_59	11	212	0.000000728837
Glycine max	Gm09	18	CH_gma_35	10	58	0.0000000000292614
Gossypium raimondii	Chr02	17	CH_gra_354	3	3	0.000676219
Gossypium raimondii	Chr05	17	CH_gra_30	10	13	1.14874e-19
Gossypium raimondii	Chr07	17	CH_gra_352	3	3	0.000676219
Gossypium raimondii	Chr08	17	CH_gra_353	3	3	0.000676219
Gossypium raimondii	Chr11	17	CH_gra_49	8	9	6.16749e-16
Gossypium raimondii	Chr13	17	CH_gra_60	7	7	0.0000000000000278446
Gossypium raimondii	Chr05	18	CH_gra_28	10	13	1.14874e-19
Manihot esculenta	scaffold03235	17	CH_mes_29	6	7	0.0000000000174905
Manihot esculenta	scaffold07478	17	CH_mes_17	7	7	0.00000000000000514194
Manihot esculenta	scaffold08265	17	CH_mes_180	3	3	0.000252165
Oryza sativa ssp. japonica	1	17	CH_osa_169	4	4	0.000000279697
Oryza sativa ssp. japonica	11	17	CH_osa_337	4	12	0.000137149
Oryza sativa ssp. japonica	3	17	CH_osa_349	3	3	0.000190327
Oryza sativa ssp. japonica	4	17	CH_osa_62	7	18	0.0000000000258749
Oryza sativa ssp. japonica	5	17	CH_osa_350	3	3	0.000190327
Oryza sativa ssp. japonica	6	17	CH_osa_56	7	15	0.00000000000525159
Oryza sativa ssp. japonica	8	17	CH_osa_351	3	3	0.000190327
Populus trichocarpa	Chr01	17	CH_ptr_3	20	22	1.48199e-42
Populus trichocarpa	Chr04	17	CH_ptr_289	6	21	0.00000633837
Populus trichocarpa	Chr05	17	CH_ptr_301	4	4	0.00000866466
Populus trichocarpa	Chr07	17	CH_ptr_81	8	11	0.000000000000275906
Populus trichocarpa	Chr11	17	CH_ptr_1	30	37	8.88763e-63
Populus trichocarpa	Chr01	18	CH_ptr_6	20	22	1.48199e-42
Populus trichocarpa	Chr11	18	CH_ptr_2	38	53	3.8335e-77
Prunus persica	scaffold_1	17	CH_ppe_266	5	11	0.00000562554
Prunus persica	scaffold_4	17	CH_ppe_1	30	33	1.40708e-68
Prunus persica	scaffold_6	17	CH_ppe_90	8	16	0.00000000000531795
Prunus persica	scaffold_7	17	CH_ppe_37	10	14	4.1633e-18
Prunus persica	scaffold_8	17	CH_ppe_253	4	4	0.00000373335
Prunus persica	scaffold_4	18	CH_ppe_1	30	33	1.40708e-68
Prunus persica	scaffold_7	18	CH_ppe_32	10	14	4.1633e-18
Ricinus communis	29676	17	CH_rco_18	8	11	0.0000000000000201251
Ricinus communis	29756	17	CH_rco_26	7	9	0.00000000000157239
Ricinus communis	30075	17	CH_rco_3	14	20	1.54251e-27
Ricinus communis	30075	18	CH_rco_3	14	20	1.54251e-27
Solanum lycopersicum	ch01	17	CH_sly_98	7	15	0.000000000335066
Solanum lycopersicum	ch01	17	CH_sly_228	4	4	0.00000243552
Solanum lycopersicum	ch02	17	CH_sly_15	11	15	3.77348e-21
Solanum lycopersicum	ch02	17	CH_sly_128	5	5	0.00000000687367
Solanum lycopersicum	ch03	17	CH_sly_127	5	5	0.00000000687367
Solanum lycopersicum	ch03	17	CH_sly_473	3	3	0.000854279
Solanum lycopersicum	ch06	17	CH_sly_474	3	3	0.000854279
Solanum lycopersicum	ch10	17	CH_sly_43	8	10	0.00000000000000650483
Solanum lycopersicum	ch01	18	CH_sly_77	11	248	0.00000684048
Solanum lycopersicum	ch02	18	CH_sly_14	11	15	3.77348e-21
Vitis vinifera	chr10	17	CH_vvi_87	9	21	0.0000000000010297
Vitis vinifera	chr13	17	CH_vvi_288	4	5	0.00002797
Vitis vinifera	chr3	17	CH_vvi_80	7	7	0.000000000000281795
Vitis vinifera	chr3	17	CH_vvi_347	5	18	0.000172084
Vitis vinifera	chr3	17	CH_vvi_427	4	9	0.00069637
Vitis vinifera	chr6	17	CH_vvi_11	16	20	9.60234e-32
Vitis vinifera	chrUn	17	CH_vvi_90	7	8	0.00000000000224715
Vitis vinifera	chr10	18	CH_vvi_66	10	77	0.0000000113862
Vitis vinifera	chr6	18	CH_vvi_12	16	20	9.60234e-32
Zea mays	3	17	CH_zma_82	4	4	0.000000227324
Zea mays	6	17	CH_zma_267	3	4	0.000601953
Zea mays	7	17	CH_zma_241	4	16	0.000407752
Zea mays	9	17	CH_zma_268	3	4	0.000601953

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