PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Chlamydomonas reinhardtii	chromosome_14	1	CH_cre_48	3	6	0.000213733
Chlamydomonas reinhardtii	chromosome_14	7	CH_cre_8	3	6	0.000123637
Oryza sativa ssp. japonica	2	3	CH_osa_233	4	5	0.00000470377
Solanum lycopersicum	ch06	3	CH_sly_249	6	14	0.00000060783
Solanum tuberosum	chr06	3	CH_stu_569	5	13	0.000071103
Vitis vinifera	chr14	3	CH_vvi_368	4	7	0.000159999

GO term	Description	Number of clusters
GO:0000228	nuclear chromosome	2
GO:0000775	chromosome, centromeric region	2
GO:0000776	kinetochore	1
GO:0000779	condensed chromosome, centromeric region	1
GO:0000784	nuclear chromosome, telomeric region	4
GO:0000785	chromatin	6
GO:0000786	nucleosome	102
GO:0000795	synaptonemal complex	4
GO:0000796	condensin complex	20
GO:0000811	GINS complex	1
GO:0005657	replication fork	2
GO:0005662	DNA replication factor A complex	2
GO:0005664	nuclear origin of replication recognition complex	11
GO:0005720	nuclear heterochromatin	2
GO:0010370	perinucleolar chromocenter	4
GO:0030896	checkpoint clamp complex	3
GO:0030915	Smc5-Smc6 complex	7
GO:0031011	Ino80 complex	11
GO:0033557	Slx1-Slx4 complex	1
GO:0043596	nuclear replication fork	4
GO:0043601	nuclear replisome	1
GO:0044427	chromosomal part	23

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