PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Malus domestica	12	3	CH_mdo_221	12	56	0.0000972457
Malus domestica	12	6	CH_mdo_42	12	56	0.0000972457
Medicago truncatula	chr3	4	CH_mtr_171	11	283	0.00015631
Medicago truncatula	chr3	5	CH_mtr_222	11	283	0.000635042
Oryza sativa ssp. japonica	3	3	CH_osa_386	5	5	0.000198537
Solanum lycopersicum	ch10	4	CH_sly_105	13	257	0.00041972
Solanum lycopersicum	ch10	5	CH_sly_101	14	257	0.000183762
Solanum tuberosum	chr10	4	CH_stu_155	13	283	0.000524009
Solanum tuberosum	chr10	5	CH_stu_165	14	283	0.000243714
Zea mays	1	4	CH_zma_21	10	73	0.00000369746
Zea mays	1	5	CH_zma_23	10	73	0.00000640565

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0006269	DNA replication, synthesis of RNA primer	8
GO:0006351	transcription, DNA-templated	38
GO:0006352	DNA-dependent transcription, initiation	11
GO:0006353	DNA-dependent transcription, termination	6
GO:0006354	DNA-dependent transcription, elongation	12
GO:0006355	regulation of transcription, DNA-dependent	118
GO:0006357	regulation of transcription from RNA polymerase II promoter	4
GO:0006366	transcription from RNA polymerase II promoter	3
GO:0006367	transcription initiation from RNA polymerase II promoter	12
GO:0006383	transcription from RNA polymerase III promoter	7
GO:0009301	snRNA transcription	4
GO:0031564	transcription antitermination	2
GO:0031935	regulation of chromatin silencing	6
GO:0032784	regulation of DNA-dependent transcription, elongation	11
GO:0032786	positive regulation of DNA-dependent transcription, elongation	1
GO:0045014	negative regulation of transcription by glucose	2
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045893	positive regulation of transcription, DNA-dependent	4
GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	7
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8

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