PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	1	13	CH_ath_308	4	5	0.000010048
Arabidopsis thaliana	1	13	CH_ath_255	4	4	0.00000201403
Arabidopsis thaliana	1	13	CH_ath_549	3	3	0.000735558
Arabidopsis thaliana	5	13	CH_ath_256	4	4	0.00000201403
Brachypodium distachyon	Bd3	13	CH_bdi_443	3	3	0.000642767
Brachypodium distachyon	Bd3	13	CH_bdi_444	3	3	0.000642767
Brachypodium distachyon	Bd3	15	CH_bdi_22	3	3	0.00042343
Carica papaya	supercontig_162	13	CH_cpa_149	4	5	0.00000503141
Oryza sativa ssp. indica	Chr06	13	CH_osaindica_220	5	5	0.000000000467278
Oryza sativa ssp. indica	Chr10	13	CH_osaindica_87	8	12	7.1533e-16
Oryza sativa ssp. indica	Chr06	15	CH_osaindica_72	3	4	0.000324326
Oryza sativa ssp. japonica	6	13	CH_osa_86	8	14	0.00000000000000366989
Populus trichocarpa	Chr11	13	CH_ptr_433	5	10	0.00000478046
Setaria italica	scaffold_3	13	CH_sit_753	3	3	0.000794465
Setaria italica	scaffold_9	13	CH_sit_207	5	5	0.00000000600123
Solanum lycopersicum	ch07	13	CH_sly_764	4	8	0.000653977
Vitis vinifera	chr11	13	CH_vvi_394	4	4	0.0000088246
Vitis vinifera	chr9	13	CH_vvi_85	8	8	0.00000000000000253835

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