PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	4	13	CH_ath_548	5	9	0.000643229
Oryza sativa ssp. indica	Chr09	13	CH_osaindica_102	9	9	0.0000000000000147452
Oryza sativa ssp. indica	Chr02	14	CH_osaindica_116	12	144	0.000334921
Oryza sativa ssp. indica	Chr09	14	CH_osaindica_72	10	15	0.000000000000363748
Oryza sativa ssp. japonica	7	13	CH_osa_391	6	9	0.00000124346
Oryza sativa ssp. japonica	7	14	CH_osa_123	10	75	0.0000312809
Oryza sativa ssp. japonica	9	14	CH_osa_104	12	84	0.000000251256
Populus trichocarpa	Chr02	13	CH_ptr_305	8	13	0.0000000924276
Populus trichocarpa	Chr14	13	CH_ptr_496	5	5	0.0000256769
Populus trichocarpa	Chr14	13	CH_ptr_691	6	12	0.000317509
Populus trichocarpa	Chr01	14	CH_ptr_78	11	15	0.00000000000029125
Populus trichocarpa	Chr02	14	CH_ptr_88	21	156	0.000000000640929
Populus trichocarpa	Chr09	14	CH_ptr_110	10	60	0.000616846
Solanum lycopersicum	ch01	13	CH_sly_96	10	11	0.0000000000000402941
Solanum lycopersicum	ch01	14	CH_sly_47	10	11	0.0000000000000402941
Vitis vinifera	chr16	13	CH_vvi_664	5	7	0.000745205
Vitis vinifera	chr15	14	CH_vvi_66	11	24	0.00000000160901
Vitis vinifera	chr3	14	CH_vvi_88	10	47	0.000139877
Vitis vinifera	chr5	14	CH_vvi_89	10	48	0.000174026
Zea mays	9	13	CH_zma_211	6	8	0.00000266668

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