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_183	5	39	0.000050864
Brachypodium distachyon	Bd3	17	CH_bdi_152	4	9	0.00000950027
Brachypodium distachyon	Bd3	17	CH_bdi_221	3	4	0.000243365
Brachypodium distachyon	Bd4	17	CH_bdi_37	6	10	0.000000000022356
Oryza sativa ssp. japonica	1	17	CH_osa_159	6	71	0.000000168126
Oryza sativa ssp. japonica	5	17	CH_osa_297	3	4	0.0000382155
Populus trichocarpa	Chr01	17	CH_ptr_470	3	4	0.000685076
Populus trichocarpa	Chr05	17	CH_ptr_380	3	3	0.000171476
Populus trichocarpa	Chr06	17	CH_ptr_381	3	3	0.000171476
Populus trichocarpa	Chr15	17	CH_ptr_245	4	5	0.00000134822
Populus trichocarpa	Chr16	17	CH_ptr_222	7	62	0.000000437543
Populus trichocarpa	Chr19	17	CH_ptr_130	5	5	0.000000000418353
Setaria italica	scaffold_5	17	CH_sit_289	6	60	0.000024662
Setaria italica	scaffold_8	17	CH_sit_2	22	51	2.9376e-45
Setaria italica	scaffold_8	18	CH_sit_2	22	51	2.9376e-45
Solanum lycopersicum	ch05	17	CH_sly_104	5	7	0.00000000065233
Solanum lycopersicum	ch06	17	CH_sly_313	3	3	0.0000355245
Vitis vinifera	chr18	17	CH_vvi_65	11	55	0.00000000000000961046
Vitis vinifera	chr18_random	17	CH_vvi_49	12	55	6.58736e-17
Vitis vinifera	chr7	17	CH_vvi_201	5	11	0.000000626849
Vitis vinifera	chr8	17	CH_vvi_180	5	9	0.000000171569
Vitis vinifera	chr18	18	CH_vvi_44	11	55	0.00000000000000961046
Zea mays	3	17	CH_zma_75	5	41	0.000000544911

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