PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: InterPro domain
Identifier: IPR002885
Description: Pentatricopeptide repeat

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00029	13	CH_atr_378	5	5	0.00018191
Amborella trichopoda	scaffold00074	13	CH_atr_93	10	12	0.0000000000793568
Amborella trichopoda	scaffold00029	14	CH_atr_43	17	119	0.0000766714
Amborella trichopoda	scaffold00074	14	CH_atr_33	10	12	0.0000000000793568
Arabidopsis thaliana	1	13	CH_ath_346	11	63	0.0000383153
Arabidopsis thaliana	1	14	CH_ath_39	15	100	0.000000352172
Beta vulgaris	Bvchr4.sca003	13	CH_bvu_162	15	74	0.000000237753
Beta vulgaris	Bvchr4.sca004	13	CH_bvu_201	14	72	0.000002104
Beta vulgaris	Bvchr4.sca003	14	CH_bvu_14	23	161	0.00000000198129
Beta vulgaris	Bvchr4.sca004	14	CH_bvu_17	16	90	0.000000402548
Capsella rubella	scaffold_2	14	CH_cru_57	21	265	0.00029204
Eucalyptus grandis	scaffold_1	13	CH_egr_174	19	44	4.33058e-18
Eucalyptus grandis	scaffold_1	14	CH_egr_132	19	44	4.33058e-18
Fragaria vesca	LG5	13	CH_fve_298	13	62	0.00000139335
Fragaria vesca	LG6	13	CH_fve_668	6	12	0.000739052
Fragaria vesca	LG5	14	CH_fve_50	13	62	0.00000139335
Glycine max	Gm09	13	CH_gma_162	14	40	0.000000000073636
Glycine max	Gm09	14	CH_gma_50	14	40	0.000000000073636
Gossypium raimondii	Chr09	13	CH_gra_29	27	79	1.22352e-24
Gossypium raimondii	Chr09	14	CH_gra_26	30	91	3.37506e-27
Lotus japonicus	chr1	13	CH_lja_307	7	36	0.000861
Lotus japonicus	chr1	13	CH_lja_273	7	33	0.000450916
Lotus japonicus	chr2	13	CH_lja_277	8	51	0.0005134
Malus domestica	17	13	CH_mdo_211	8	18	0.00000259939
Malus domestica	9	13	CH_mdo_335	9	37	0.0000822153
Malus domestica	9	13	CH_mdo_436	11	72	0.000253301
Malus domestica	15	14	CH_mdo_31	13	114	0.000415323
Malus domestica	9	14	CH_mdo_34	10	60	0.000524181
Malus domestica	9	14	CH_mdo_30	11	72	0.000253301
Medicago truncatula	chr4	13	CH_mtr_966	5	7	0.000174832
Medicago truncatula	chr6	13	CH_mtr_28	26	56	8.46296e-32
Medicago truncatula	chr6	13	CH_mtr_744	6	10	0.0000180076
Medicago truncatula	chr6	13	CH_mtr_958	10	68	0.000153163
Medicago truncatula	chr7	13	CH_mtr_965	5	7	0.000174832
Medicago truncatula	chr1	14	CH_mtr_166	18	261	0.0000353897
Medicago truncatula	chr6	14	CH_mtr_28	26	56	8.46296e-32
Medicago truncatula	chr6	14	CH_mtr_170	16	207	0.0000616626
Oryza sativa ssp. japonica	10	13	CH_osa_397	11	70	0.00000145426
Oryza sativa ssp. japonica	10	14	CH_osa_103	17	202	0.000000194185
Populus trichocarpa	Chr05	13	CH_ptr_306	13	56	0.0000000951625
Populus trichocarpa	Chr05	14	CH_ptr_95	13	56	0.0000000951625
Prunus persica	scaffold_6	13	CH_ppe_650	6	10	0.000328578
Prunus persica	scaffold_6	14	CH_ppe_105	21	205	0.0000284732
Ricinus communis	29938	13	CH_rco_315	6	9	0.000112123
Solanum tuberosum	chr06	13	CH_stu_501	7	10	0.00000066615
Solanum tuberosum	chr06	13	CH_stu_413	7	8	0.0000000455857
Solanum tuberosum	chr07	13	CH_stu_637	6	8	0.0000106222
Solanum tuberosum	chr09	13	CH_stu_709	6	9	0.0000314606
Solanum tuberosum	chr11	13	CH_stu_810	6	10	0.00007765
Solanum tuberosum	chr06	14	CH_stu_137	19	200	0.00000819413
Zea mays	2	13	CH_zma_52	14	42	0.00000000000720367
Zea mays	2	14	CH_zma_17	14	42	0.00000000000720367

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