PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0005634
Description: nucleus

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	3	4	CH_ath_30	129	268	0.000000141103
Arabidopsis thaliana	3	5	CH_ath_47	130	268	0.000000359472
Arabidopsis thaliana	5	5	CH_ath_100	135	300	0.0000844856
Arabidopsis thaliana	3	6	CH_ath_57	130	268	0.000000493113
Arabidopsis thaliana	5	6	CH_ath_113	135	300	0.000113125
Arabidopsis thaliana	5	10	CH_ath_31	79	192	0.000107627
Arabidopsis thaliana	5	11	CH_ath_33	80	192	0.00009942
Arabidopsis thaliana	5	12	CH_ath_36	80	192	0.000119646
Capsella rubella	scaffold_1	2	CH_cru_282	8	8	0.000234847
Carica papaya	supercontig_50	3	CH_cpa_371	17	48	0.000977234
Carica papaya	supercontig_50	6	CH_cpa_39	17	48	0.000977234
Eucalyptus grandis	scaffold_10	2	CH_egr_721	19	71	0.0003092
Eucalyptus grandis	scaffold_10	3	CH_egr_878	19	71	0.000879435
Eucalyptus grandis	scaffold_10	5	CH_egr_269	19	71	0.0003092
Eucalyptus grandis	scaffold_10	6	CH_egr_319	19	71	0.000879435
Eucalyptus grandis	scaffold_7	6	CH_egr_161	14	17	0.000000000156633
Medicago truncatula	chr1	1	CH_mtr_367	6	9	0.0000233128
Medicago truncatula	chr3	1	CH_mtr_440	6	11	0.000125432
Medicago truncatula	chr3	4	CH_mtr_189	10	61	0.000375548
Medicago truncatula	chr4	5	CH_mtr_145	28	187	0.00000943156
Medicago truncatula	chr7	6	CH_mtr_139	10	14	0.000000617438
Oryza sativa ssp. japonica	4	5	CH_osa_176	21	127	0.000884004
Oryza sativa ssp. japonica	4	11	CH_osa_56	21	127	0.0000626784
Oryza sativa ssp. japonica	4	12	CH_osa_68	21	127	0.000170016
Populus trichocarpa	Chr03	1	CH_ptr_217	8	13	0.00000783992
Solanum lycopersicum	ch02	1	CH_sly_440	5	5	0.000999866
Solanum lycopersicum	ch03	1	CH_sly_169	18	73	0.000000241437
Solanum lycopersicum	ch03	2	CH_sly_315	22	73	0.0000626272
Solanum lycopersicum	ch03	3	CH_sly_377	23	73	0.0000360393
Solanum lycopersicum	ch03	4	CH_sly_59	18	73	0.000000241437
Solanum lycopersicum	ch03	5	CH_sly_90	28	113	0.0000603814
Solanum lycopersicum	ch03	6	CH_sly_115	30	113	0.0000125117
Zea mays	1	5	CH_zma_40	42	294	0.000868208
Zea mays	2	6	CH_zma_48	10	17	0.000365966

Available child term results

GO term	Description	Number of clusters
GO:0000124	SAGA complex	5
GO:0000228	nuclear chromosome	2
GO:0000418	DNA-directed RNA polymerase IV complex	2
GO:0000419	DNA-directed RNA polymerase V complex	2
GO:0000439	core TFIIH complex	3
GO:0000445	THO complex part of transcription export complex	3
GO:0000784	nuclear chromosome, telomeric region	4
GO:0000795	synaptonemal complex	4
GO:0000811	GINS complex	1
GO:0005643	nuclear pore	21
GO:0005652	nuclear lamina	2
GO:0005654	nucleoplasm	1
GO:0005662	DNA replication factor A complex	2
GO:0005664	nuclear origin of replication recognition complex	11
GO:0005665	DNA-directed RNA polymerase II, core complex	1
GO:0005669	transcription factor TFIID complex	2
GO:0005672	transcription factor TFIIA complex	9
GO:0005673	transcription factor TFIIE complex	3
GO:0005674	transcription factor TFIIF complex	10
GO:0005680	anaphase-promoting complex	11
GO:0005681	spliceosomal complex	7
GO:0005720	nuclear heterochromatin	2
GO:0005847	mRNA cleavage and polyadenylation specificity factor complex	18
GO:0005849	mRNA cleavage factor complex	2
GO:0008180	COP9 signalosome	1
GO:0016363	nuclear matrix	5
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	3
GO:0016592	mediator complex	2
GO:0016602	CCAAT-binding factor complex	19
GO:0016604	nuclear body	4
GO:0017053	transcriptional repressor complex	8
GO:0030870	Mre11 complex	6
GO:0030896	checkpoint clamp complex	3
GO:0031011	Ino80 complex	11
GO:0031261	DNA replication preinitiation complex	3
GO:0031519	PcG protein complex	7
GO:0031965	nuclear membrane	1
GO:0031981	nuclear lumen	1
GO:0032039	integrator complex	4
GO:0032389	MutLalpha complex	9
GO:0032777	Piccolo NuA4 histone acetyltransferase complex	9
GO:0032783	ELL-EAF complex	3
GO:0033557	Slx1-Slx4 complex	1
GO:0033597	mitotic checkpoint complex	7
GO:0034399	nuclear periphery	2
GO:0035101	FACT complex	26
GO:0043078	polar nucleus	4
GO:0043189	H4/H2A histone acetyltransferase complex	3
GO:0043564	Ku70:Ku80 complex	8
GO:0043596	nuclear replication fork	4
GO:0043601	nuclear replisome	1
GO:0044428	nuclear part	1
GO:0044451	nucleoplasm part	1
GO:0046540	U4/U6 x U5 tri-snRNP complex	5
GO:0048188	Set1C/COMPASS complex	2
GO:0070461	SAGA-type complex	5
GO:0070531	BRCA1-A complex	7

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