PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Brachypodium distachyon	Bd2	17	CH_bdi_60	5	7	0.0000000025511
Brachypodium distachyon	Bd3	17	CH_bdi_224	3	4	0.000287523
Chlamydomonas reinhardtii	chromosome_1	17	CH_cre_63	3	10	0.000663996
Oryza sativa ssp. japonica	10	17	CH_osa_74	5	6	0.0000000000906838
Oryza sativa ssp. japonica	11	17	CH_osa_400	3	6	0.000545919
Oryza sativa ssp. japonica	5	17	CH_osa_241	4	11	0.0000067632
Oryza sativa ssp. japonica	8	17	CH_osa_182	4	7	0.00000071905
Oryza sativa ssp. japonica	11	19	CH_osa_28	3	6	0.000190922
Oryza sativa ssp. japonica	8	19	CH_osa_7	4	7	0.00000017364
Populus trichocarpa	Chr10	17	CH_ptr_350	3	3	0.0000568838
Populus trichocarpa	Chr13	17	CH_ptr_195	4	4	0.0000000611302
Populus trichocarpa	scaffold_32	17	CH_ptr_395	3	4	0.000227346
Setaria italica	scaffold_3	17	CH_sit_201	4	8	0.00000173374
Setaria italica	scaffold_6	17	CH_sit_301	3	3	0.0000474424
Setaria italica	scaffold_6	17	CH_sit_224	4	10	0.00000346456
Setaria italica	scaffold_9	17	CH_sit_410	3	6	0.000473652
Setaria italica	scaffold_9	17	CH_sit_200	4	7	0.00000173374
Solanum lycopersicum	ch01	17	CH_sly_315	3	3	0.000038659
Solanum lycopersicum	ch05	17	CH_sly_365	3	4	0.000154518
Vitis vinifera	chr12	17	CH_vvi_332	3	3	0.000114941
Vitis vinifera	chr5	17	CH_vvi_112	5	5	0.000000000272701
Vitis vinifera	chr7	17	CH_vvi_182	4	4	0.00000017924
Zea mays	5	17	CH_zma_140	3	5	0.0000653822

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