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_296	3	3	0.0000655819
Brachypodium distachyon	Bd1	17	CH_bdi_228	3	4	0.000336719
Brachypodium distachyon	Bd1	17	CH_bdi_103	4	5	0.000000587182
Brachypodium distachyon	Bd3	17	CH_bdi_89	4	4	0.000000117569
Brachypodium distachyon	Bd4	17	CH_bdi_17	7	8	0.00000000000000215809
Populus trichocarpa	Chr01	17	CH_ptr_99	7	10	0.00000000000771317
Populus trichocarpa	Chr02	17	CH_ptr_262	4	4	0.00000287467
Populus trichocarpa	Chr05	17	CH_ptr_223	5	8	0.000000455395
Populus trichocarpa	Chr06	17	CH_ptr_70	10	29	0.0000000000000257129
Populus trichocarpa	Chr06	17	CH_ptr_115	8	23	0.0000000000848765
Populus trichocarpa	Chr11	17	CH_ptr_312	4	5	0.0000143402
Populus trichocarpa	Chr18	17	CH_ptr_2	24	35	2.48525e-49
Populus trichocarpa	Chr06	18	CH_ptr_52	10	29	0.0000000000000257129
Populus trichocarpa	Chr18	18	CH_ptr_4	24	35	2.48525e-49
Setaria italica	scaffold_1	17	CH_sit_183	4	5	0.000000484129
Setaria italica	scaffold_2	17	CH_sit_54	7	12	0.000000000000128073
Setaria italica	scaffold_4	17	CH_sit_391	3	4	0.000311149
Setaria italica	scaffold_4	17	CH_sit_90	5	5	0.000000000117911
Vitis vinifera	chr16	17	CH_vvi_381	3	3	0.000328228
Vitis vinifera	chr18	17	CH_vvi_195	5	10	0.000000405711
Vitis vinifera	chr4	17	CH_vvi_7	17	25	5.40331e-36
Vitis vinifera	chr4	18	CH_vvi_7	17	25	5.40331e-36

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