PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	2	17	CH_ath_259	3	3	0.0000194179
Arabidopsis thaliana	5	17	CH_ath_139	4	4	0.0000000150258
Brachypodium distachyon	Bd5	17	CH_bdi_87	4	5	0.0000000960946
Chlamydomonas reinhardtii	chromosome_16	17	CH_cre_53	3	4	0.000201684
Chlamydomonas reinhardtii	chromosome_2	17	CH_cre_21	4	5	0.000000329842
Oryza sativa ssp. japonica	3	17	CH_osa_270	3	4	0.0000225379
Oryza sativa ssp. japonica	6	17	CH_osa_232	3	3	0.00000563639
Populus trichocarpa	Chr05	17	CH_ptr_344	3	3	0.000049629
Populus trichocarpa	Chr10	17	CH_ptr_305	4	10	0.0000106264
Populus trichocarpa	Chr10	17	CH_ptr_232	4	6	0.00000076154
Setaria italica	scaffold_7	17	CH_sit_379	3	6	0.00024931
Solanum lycopersicum	ch02	17	CH_sly_135	4	4	0.0000000117347
Vitis vinifera	chr1	17	CH_vvi_176	4	5	0.000000135068
Vitis vinifera	chr5	17	CH_vvi_289	3	3	0.0000284314
Zea mays	2	17	CH_zma_57	4	5	0.0000000433335

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