PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Beta vulgaris	Bvchr9.sca001	5	CH_bvu_13	11	42	0.00000000297795
Beta vulgaris	Bvchr9.sca001	6	CH_bvu_20	11	42	0.00000000486869
Oryza sativa ssp. japonica	3	1	CH_osa_29	11	47	6.08355e-17

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0010495	long-distance posttranscriptional gene silencing	4
GO:0016246	RNA interference	2
GO:0017148	negative regulation of translation	1
GO:0031047	gene silencing by RNA	12
GO:0031054	pre-miRNA processing	2
GO:0031935	regulation of chromatin silencing	6
GO:0035067	negative regulation of histone acetylation	8
GO:0035196	production of miRNAs involved in gene silencing by miRNA	2
GO:0035278	negative regulation of translation involved in gene silencing by miRNA	18
GO:0035279	mRNA cleavage involved in gene silencing by miRNA	6
GO:0042177	negative regulation of protein catabolic process	2
GO:0045014	negative regulation of transcription by glucose	2
GO:0045128	negative regulation of reciprocal meiotic recombination	4
GO:0045814	negative regulation of gene expression, epigenetic	2
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045900	negative regulation of translational elongation	3
GO:0045910	negative regulation of DNA recombination	2
GO:0051444	negative regulation of ubiquitin-protein ligase activity	4
GO:0060148	positive regulation of posttranscriptional gene silencing	4
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8
GO:2000113	negative regulation of cellular macromolecule biosynthetic process	2

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