PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	17	CH_ath_386	9	56	0.000806646
Brachypodium distachyon	Bd3	18	CH_bdi_27	15	110	0.00000125479
Oryza sativa ssp. japonica	6	17	CH_osa_271	5	6	0.000022684
Populus trichocarpa	Chr01	18	CH_ptr_59	11	15	0.00000000000101751
Populus trichocarpa	Chr01	18	CH_ptr_88	14	81	0.00000216158
Populus trichocarpa	Chr09	18	CH_ptr_107	13	87	0.0000686902
Setaria italica	scaffold_2	18	CH_sit_73	10	47	0.0000896
Setaria italica	scaffold_5	18	CH_sit_80	10	53	0.000310099
Setaria italica	scaffold_6	18	CH_sit_40	12	27	0.0000000000967505
Setaria italica	scaffold_8	18	CH_sit_58	10	33	0.00000195067
Solanum lycopersicum	ch08	17	CH_sly_243	7	12	0.0000039061
Solanum lycopersicum	ch11	18	CH_sly_86	16	160	0.0000859504
Vitis vinifera	chrUn	17	CH_vvi_55	18	35	8.24195e-16
Vitis vinifera	chr12	18	CH_vvi_82	15	61	0.000000462585
Vitis vinifera	chr18	18	CH_vvi_62	11	19	0.00000000338133
Vitis vinifera	chr4	18	CH_vvi_102	11	43	0.000149508
Vitis vinifera	chrUn	18	CH_vvi_40	18	35	8.24195e-16
Zea mays	1	17	CH_zma_196	6	16	0.000361379
Zea mays	10	17	CH_zma_205	4	4	0.000419878
Zea mays	3	18	CH_zma_29	12	115	0.000168534

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