PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	13	CH_ath_406	4	9	0.000076824
Brachypodium distachyon	Bd3	13	CH_bdi_240	4	5	0.00000769097
Oryza sativa ssp. indica	Chr01	13	CH_osaindica_556	4	8	0.0000217659
Oryza sativa ssp. indica	Chr02	13	CH_osaindica_379	4	4	0.000000312457
Oryza sativa ssp. japonica	2	13	CH_osa_207	5	6	0.00000000134636
Physcomitrella patens	scaffold_57	13	CH_ppa_3	8	11	0.0000000000000137214
Physcomitrella patens	scaffold_57	15	CH_ppa_11	4	11	0.000343107
Populus trichocarpa	Chr06	13	CH_ptr_21	16	22	8.42801e-32
Populus trichocarpa	Chr17	13	CH_ptr_299	5	6	0.0000000647698
Populus trichocarpa	Chr06	14	CH_ptr_22	16	22	8.42801e-32
Setaria italica	scaffold_1	13	CH_sit_423	4	6	0.00000976831
Sorghum bicolor	chr_3	13	CH_sbi_622	3	3	0.000371098
Vitis vinifera	chr16	13	CH_vvi_211	5	6	0.0000000173947
Vitis vinifera	chrUn	13	CH_vvi_141	6	7	0.0000000000496114

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