PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0010468
Description: regulation of gene expression

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_2	5	CH_aly_51	46	263	0.0000451168
Arabidopsis lyrata	scaffold_2	6	CH_aly_77	46	263	0.000155813
Capsella rubella	scaffold_2	5	CH_cru_80	42	214	0.000668541
Capsella rubella	scaffold_2	11	CH_cru_1	42	232	0.0000417431
Capsella rubella	scaffold_2	12	CH_cru_1	42	232	0.0000880024
Eucalyptus grandis	scaffold_9	1	CH_egr_307	13	35	0.000000127308
Eucalyptus grandis	scaffold_9	4	CH_egr_159	13	35	0.000000127308
Gossypium raimondii	Chr08	2	CH_gra_349	13	28	0.000796065
Lotus japonicus	chr2	2	CH_lja_56	12	32	0.00000257227
Lotus japonicus	chr2	5	CH_lja_8	12	32	0.00000257227
Medicago truncatula	chr1	6	CH_mtr_235	30	251	0.000218609
Physcomitrella patens	scaffold_31	5	CH_ppa_4	21	105	0.0000399325
Physcomitrella patens	scaffold_31	6	CH_ppa_6	21	105	0.000109079
Populus trichocarpa	Chr06	3	CH_ptr_222	18	37	0.000000107809
Populus trichocarpa	Chr06	6	CH_ptr_91	18	37	0.000000107809
Thellungiella parvula	ch5-6	2	CH_tpa_135	8	9	0.000111853
Thellungiella parvula	ch5-6	2	CH_tpa_178	21	74	0.000435003
Thellungiella parvula	ch5-6	5	CH_tpa_16	43	208	0.00000203377
Thellungiella parvula	ch5-6	6	CH_tpa_16	44	208	0.00000306455
Vitis vinifera	chr4	3	CH_vvi_370	19	72	0.000170461
Vitis vinifera	chr13_random	5	CH_vvi_87	14	40	0.000075902
Vitis vinifera	chr13_random	6	CH_vvi_127	14	40	0.000309064
Vitis vinifera	chr4	6	CH_vvi_122	23	102	0.00012544

Available child term results

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0006306	DNA methylation	5
GO:0006355	regulation of transcription, DNA-dependent	118
GO:0006357	regulation of transcription from RNA polymerase II promoter	4
GO:0006450	regulation of translational fidelity	4
GO:0010424	DNA methylation on cytosine within a CG sequence	4
GO:0010495	long-distance posttranscriptional gene silencing	4
GO:0010608	posttranscriptional regulation of gene expression	2
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: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: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:0044030	regulation of DNA methylation	11
GO:0045014	negative regulation of transcription by glucose	2
GO:0045814	negative regulation of gene expression, epigenetic	2
GO:0045892	negative regulation of transcription, DNA-dependent	2
GO:0045893	positive regulation of transcription, DNA-dependent	4
GO:0045900	negative regulation of translational elongation	3
GO:0045901	positive regulation of translational elongation	3
GO:0048024	regulation of mRNA splicing, via spliceosome	2
GO:0050821	protein stabilization	2
GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	7
GO:0060148	positive regulation of posttranscriptional gene silencing	4
GO:0090309	positive regulation of methylation-dependent chromatin silencing	8
GO:1900363	regulation of mRNA polyadenylation	2

Functional clusters experiments

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