PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0043565
Description: sequence-specific DNA binding

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Capsella rubella	scaffold_6	1	CH_cru_122	6	7	0.00000678122
Capsella rubella	scaffold_6	2	CH_cru_179	6	7	0.000016888
Capsella rubella	scaffold_6	3	CH_cru_218	6	7	0.0000195835
Carica papaya	supercontig_106	1	CH_cpa_163	4	4	0.000576995
Carica papaya	supercontig_117	1	CH_cpa_156	5	8	0.000400997
Carica papaya	supercontig_117	2	CH_cpa_223	5	8	0.000803925
Chlamydomonas reinhardtii	chromosome_9	1	CH_cre_32	5	16	0.0000362835
Chlamydomonas reinhardtii	chromosome_9	2	CH_cre_38	5	16	0.0000826817
Chlamydomonas reinhardtii	chromosome_9	3	CH_cre_75	5	16	0.000139468
Cucumis melo	CM3.5_scaffold00047	3	CH_cme_290	5	7	0.000248415
Cucumis melo	CM3.5_scaffold00047	9	CH_cme_6	5	7	0.000200782
Fragaria vesca	LG6	1	CH_fve_193	6	17	0.000110505
Glycine max	Gm11	1	CH_gma_213	7	12	0.0000211363
Glycine max	Gm18	1	CH_gma_359	6	11	0.000701803
Glycine max	Gm11	2	CH_gma_286	7	12	0.0000449631
Glycine max	Gm11	3	CH_gma_360	7	12	0.0000673196
Malus domestica	17	3	CH_mdo_333	4	4	0.000446298
Medicago truncatula	chr2	1	CH_mtr_579	5	13	0.000892197
Medicago truncatula	chr2	1	CH_mtr_353	6	14	0.000013302
Medicago truncatula	chr2	2	CH_mtr_449	6	14	0.0000317421
Oryza sativa ssp. japonica	11	1	CH_osa_266	5	8	0.0000509578
Oryza sativa ssp. japonica	5	1	CH_osa_376	4	5	0.000663342
Oryza sativa ssp. japonica	11	2	CH_osa_284	5	8	0.0000837431
Oryza sativa ssp. japonica	5	2	CH_osa_423	4	5	0.000987416
Oryza sativa ssp. japonica	11	3	CH_osa_372	5	8	0.000130155
Oryza sativa ssp. japonica	6	3	CH_osa_245	8	31	0.00000918977
Oryza sativa ssp. japonica	5	4	CH_osa_134	13	205	0.000165954
Solanum lycopersicum	ch03	1	CH_sly_422	4	4	0.000841484
Solanum lycopersicum	ch09	1	CH_sly_350	5	7	0.000214512
Solanum lycopersicum	ch05	3	CH_sly_615	8	31	0.000660186
Solanum lycopersicum	ch09	3	CH_sly_345	6	8	0.0000132099
Solanum tuberosum	chr03	1	CH_stu_243	6	7	0.000000481182
Solanum tuberosum	chr03	1	CH_stu_342	5	6	0.0000370613
Solanum tuberosum	chr03	2	CH_stu_282	6	7	0.00000129958
Solanum tuberosum	chr03	3	CH_stu_419	6	7	0.00000253989
Solanum tuberosum	chr06	3	CH_stu_746	6	13	0.000576988
Solanum tuberosum	chr09	3	CH_stu_721	5	7	0.000511501
Solanum tuberosum	chr10	3	CH_stu_443	7	12	0.00000400774
Solanum tuberosum	chr03	4	CH_stu_119	13	104	0.0000066206
Solanum tuberosum	chr03	6	CH_stu_202	12	85	0.000176287

Available child term results

GO term	Description	Number of clusters
GO:0000976	transcription regulatory region sequence-specific DNA binding	3
GO:0001164	RNA polymerase I CORE element sequence-specific DNA binding	1
GO:0008327	methyl-CpG binding	1
GO:0080084	5S rDNA binding	4

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