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_75	6	8	0.00000000000286434
Oryza sativa ssp. indica	Chr01	13	CH_osaindica_629	3	3	0.0000483112
Oryza sativa ssp. indica	Chr01	13	CH_osaindica_557	4	12	0.0000218451
Oryza sativa ssp. indica	Chr12	13	CH_osaindica_628	3	3	0.0000483112
Oryza sativa ssp. japonica	1	13	CH_osa_836	3	6	0.000842436
Oryza sativa ssp. japonica	1	13	CH_osa_665	3	4	0.000168714
Oryza sativa ssp. japonica	12	13	CH_osa_765	3	5	0.000421502
Physcomitrella patens	scaffold_1	13	CH_ppa_63	3	3	0.0000868314
Populus trichocarpa	Chr14	13	CH_ptr_198	5	5	0.000000000231014
Setaria italica	scaffold_5	13	CH_sit_553	3	3	0.000105357
Solanum lycopersicum	ch02	13	CH_sly_570	3	3	0.00014448
Solanum lycopersicum	ch02	13	CH_sly_42	10	18	8.94099e-20
Solanum lycopersicum	ch02	14	CH_sly_31	10	18	8.94099e-20
Sorghum bicolor	chr_10	13	CH_sbi_513	3	3	0.000140627
Sorghum bicolor	chr_3	13	CH_sbi_512	3	3	0.000140627
Vitis vinifera	chr14	13	CH_vvi_191	5	7	0.00000000614268
Vitis vinifera	chr16	13	CH_vvi_510	3	3	0.000120406
Vitis vinifera	chr17	13	CH_vvi_350	5	18	0.00000247084
Vitis vinifera	chr5	13	CH_vvi_209	5	8	0.0000000163593
Vitis vinifera	chr7	13	CH_vvi_636	3	4	0.000481035

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