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_200	4	9	0.00000162721
Arabidopsis thaliana	4	17	CH_ath_254	3	3	0.0000174092
Brachypodium distachyon	Bd1	17	CH_bdi_47	5	6	0.0000000000956601
Oryza sativa ssp. japonica	9	17	CH_osa_246	3	3	0.00000866173
Physcomitrella patens	scaffold_189	17	CH_ppa_4	4	5	0.0000000660592
Populus trichocarpa	Chr03	17	CH_ptr_192	4	4	0.0000000462302
Setaria italica	scaffold_2	17	CH_sit_78	5	5	0.000000000021389
Setaria italica	scaffold_2	17	CH_sit_140	4	4	0.0000000252005
Setaria italica	scaffold_2	19	CH_sit_10	3	3	0.0000140454
Solanum lycopersicum	ch08	17	CH_sly_141	4	4	0.0000000206095
Vitis vinifera	chr12	17	CH_vvi_39	9	10	5.07248e-19
Vitis vinifera	chr2	17	CH_vvi_12	15	21	1.93431e-31
Vitis vinifera	chrUn	17	CH_vvi_125	5	5	0.00000000207409
Vitis vinifera	chrUn	17	CH_vvi_264	4	6	0.0000133583
Vitis vinifera	chr2	18	CH_vvi_13	15	21	1.93431e-31
Vitis vinifera	chrUn	18	CH_vvi_81	10	174	0.000000423936
Vitis vinifera	chr2	19	CH_vvi_22	4	14	0.0000685268
Zea mays	7	17	CH_zma_195	3	5	0.000352156

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