PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	3	17	CH_ath_39	8	11	2.95774e-17
Arabidopsis thaliana	5	17	CH_ath_163	4	4	0.0000000942598
Brachypodium distachyon	Bd1	17	CH_bdi_166	4	7	0.0000203882
Brachypodium distachyon	Bd1	17	CH_bdi_69	5	7	0.0000000254112
Oryza sativa ssp. japonica	12	17	CH_osa_379	3	4	0.000305835
Oryza sativa ssp. japonica	12	17	CH_osa_205	6	53	0.00000199085
Oryza sativa ssp. japonica	7	17	CH_osa_217	4	7	0.00000287245
Oryza sativa ssp. japonica	7	17	CH_osa_309	3	3	0.0000765219
Populus trichocarpa	Chr07	17	CH_ptr_162	6	14	0.0000000104963
Setaria italica	scaffold_2	17	CH_sit_174	4	4	0.000000367901
Setaria italica	scaffold_3	17	CH_sit_440	3	4	0.000837853
Setaria italica	scaffold_3	17	CH_sit_369	3	3	0.000209745
Solanum lycopersicum	ch06	17	CH_sly_489	3	4	0.000909434
Solanum lycopersicum	ch12	17	CH_sly_490	3	4	0.000909434
Vitis vinifera	chr1	17	CH_vvi_142	7	27	0.0000000140175
Vitis vinifera	chr16	17	CH_vvi_391	3	3	0.000454712
Vitis vinifera	chr2	17	CH_vvi_317	4	8	0.0000792591
Vitis vinifera	chrUn	17	CH_vvi_390	3	3	0.000454712

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