PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0010467
Description: gene expression

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Brassica rapa	A10	3	CH_bra_59	10	13	0.00000000574538
Brassica rapa	A10	6	CH_bra_18	10	13	0.00000000574538
Capsella rubella	scaffold_1	3	CH_cru_315	5	5	0.000242381
Citrus sinensis	scaffold00001	3	CH_csi_63	7	7	0.0000000773373
Eucalyptus grandis	scaffold_1	3	CH_egr_720	5	5	0.000108267
Eucalyptus grandis	scaffold_1	3	CH_egr_126	14	16	5.73109e-18
Eucalyptus grandis	scaffold_10	3	CH_egr_145	13	15	2.55389e-16
Eucalyptus grandis	scaffold_7	3	CH_egr_150	14	19	5.25363e-16
Eucalyptus grandis	scaffold_1	6	CH_egr_91	14	16	5.73109e-18
Eucalyptus grandis	scaffold_10	6	CH_egr_100	13	15	2.55389e-16
Eucalyptus grandis	scaffold_7	6	CH_egr_102	14	19	5.25363e-16
Fragaria vesca	LG2	3	CH_fve_185	6	7	0.0000024316
Fragaria vesca	LG7	3	CH_fve_214	6	8	0.00000960356
Glycine max	Gm13	3	CH_gma_210	7	7	0.000000527504
Glycine max	Gm19	3	CH_gma_548	5	5	0.000740589
Gossypium raimondii	Chr01	3	CH_gra_129	8	8	0.0000000130424
Malus domestica	1	3	CH_mdo_53	10	21	0.00000000599085
Malus domestica	1	6	CH_mdo_14	10	21	0.00000000599085
Medicago truncatula	chr1	3	CH_mtr_287	8	12	0.000000023536
Medicago truncatula	chr1	3	CH_mtr_219	10	20	0.00000000134404
Medicago truncatula	chr6	3	CH_mtr_249	15	77	0.00000000464647
Medicago truncatula	chr7	3	CH_mtr_798	6	13	0.000478876
Medicago truncatula	chr8	3	CH_mtr_813	7	23	0.000558104
Medicago truncatula	chr1	6	CH_mtr_103	10	20	0.00000000134404
Medicago truncatula	chr6	6	CH_mtr_101	16	85	0.00000000120906
Oryza sativa ssp. japonica	11	3	CH_osa_267	5	5	0.0000208616
Physcomitrella patens	scaffold_259	3	CH_ppa_48	7	20	0.0000397228
Populus trichocarpa	Chr14	3	CH_ptr_302	6	6	0.00000419559
Populus trichocarpa	Chr14	3	CH_ptr_454	5	5	0.000193871
Prunus persica	scaffold_2	3	CH_ppe_60	13	19	0.0000000000000211276
Prunus persica	scaffold_2	6	CH_ppe_41	13	19	0.0000000000000211276
Ricinus communis	30076	3	CH_rco_157	8	16	0.00000471316
Ricinus communis	30174	3	CH_rco_187	5	5	0.0000580526
Solanum tuberosum	chr01	3	CH_stu_338	9	14	0.0000000989036
Solanum tuberosum	chr03	3	CH_stu_437	7	9	0.00000372795
Solanum tuberosum	chr12	3	CH_stu_86	13	13	1.39049e-17
Solanum tuberosum	chr12	3	CH_stu_523	6	7	0.0000327673
Solanum tuberosum	chr01	6	CH_stu_144	10	23	0.00000107683
Solanum tuberosum	chr12	6	CH_stu_68	13	13	1.39049e-17
Theobroma cacao	scaffold_1	3	CH_tca_285	5	5	0.0000493864
Vitis vinifera	chr15	3	CH_vvi_150	7	7	0.0000000176048
Vitis vinifera	chr19	3	CH_vvi_406	5	6	0.000317188
Vitis vinifera	chr7	3	CH_vvi_322	5	5	0.0000536776
Zea mays	1	3	CH_zma_257	5	5	0.000278191

Available child term results

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0000154	rRNA modification	42
GO:0000244	spliceosomal tri-snRNP complex assembly	6
GO:0000245	spliceosomal complex assembly	6
GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	6
GO:0000387	spliceosomal snRNP assembly	3
GO:0000966	RNA 5'-end processing	12
GO:0001682	tRNA 5'-leader removal	4
GO:0002098	tRNA wobble uridine modification	1
GO:0006306	DNA methylation	5
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:0006364	rRNA processing	6
GO:0006366	transcription from RNA polymerase II promoter	3
GO:0006367	transcription initiation from RNA polymerase II promoter	12
GO:0006370	7-methylguanosine mRNA capping	5
GO:0006376	mRNA splice site selection	1
GO:0006378	mRNA polyadenylation	2
GO:0006383	transcription from RNA polymerase III promoter	7
GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	3
GO:0006396	RNA processing	12
GO:0006397	mRNA processing	1
GO:0006412	translation	6
GO:0006413	translational initiation	3
GO:0006414	translational elongation	11
GO:0006418	tRNA aminoacylation for protein translation	4
GO:0006419	alanyl-tRNA aminoacylation	9
GO:0006420	arginyl-tRNA aminoacylation	11
GO:0006421	asparaginyl-tRNA aminoacylation	6
GO:0006423	cysteinyl-tRNA aminoacylation	12
GO:0006426	glycyl-tRNA aminoacylation	15
GO:0006428	isoleucyl-tRNA aminoacylation	5
GO:0006429	leucyl-tRNA aminoacylation	8
GO:0006430	lysyl-tRNA aminoacylation	11
GO:0006431	methionyl-tRNA aminoacylation	4
GO:0006432	phenylalanyl-tRNA aminoacylation	2
GO:0006433	prolyl-tRNA aminoacylation	7
GO:0006434	seryl-tRNA aminoacylation	16
GO:0006435	threonyl-tRNA aminoacylation	5
GO:0006436	tryptophanyl-tRNA aminoacylation	6
GO:0006438	valyl-tRNA aminoacylation	29
GO:0006450	regulation of translational fidelity	4
GO:0006465	signal peptide processing	3
GO:0006627	protein processing involved in protein targeting to mitochondrion	3
GO:0008033	tRNA processing	40
GO:0008380	RNA splicing	1
GO:0008616	queuosine biosynthetic process	8
GO:0009301	snRNA transcription	4
GO:0009452	7-methylguanosine RNA capping	1
GO:0010424	DNA methylation on cytosine within a CG sequence	4
GO:0010468	regulation of gene expression	23
GO:0010495	long-distance posttranscriptional gene silencing	4
GO:0010608	posttranscriptional regulation of gene expression	2
GO:0016180	snRNA processing	1
GO:0016246	RNA interference	2
GO:0016540	protein autoprocessing	10
GO:0017148	negative regulation of translation	1
GO:0031047	gene silencing by RNA	12
GO:0031054	pre-miRNA processing	2
GO:0031123	RNA 3'-end processing	2
GO:0031167	rRNA methylation	5
GO:0031425	chloroplast RNA 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:0034227	tRNA thio-modification	4
GO:0034470	ncRNA processing	4
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:0042779	tRNA 3'-trailer cleavage	1
GO:0043144	snoRNA processing	1
GO:0044030	regulation of DNA methylation	11
GO:0045014	negative regulation of transcription by glucose	2
GO:0045292	mRNA cis splicing, via spliceosome	8
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:0070526	threonylcarbamoyladenosine biosynthetic process	2
GO:0071076	RNA 3' uridylation	4
GO:0071586	CAAX-box protein processing	3
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