PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0006355
Description: regulation of transcription, DNA-dependent

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_1	2	CH_aly_192	11	18	0.0000236546
Arabidopsis lyrata	scaffold_1	5	CH_aly_46	11	18	0.0000236546
Capsella rubella	scaffold_7	1	CH_cru_170	8	11	0.000106163
Carica papaya	supercontig_80	1	CH_cpa_116	8	12	0.000103662
Carica papaya	supercontig_80	2	CH_cpa_153	9	14	0.000161887
Carica papaya	supercontig_80	3	CH_cpa_79	11	14	0.000000194582
Carica papaya	supercontig_80	6	CH_cpa_21	11	14	0.000000194582
Citrus sinensis	scaffold00167	1	CH_csi_80	9	13	0.00000644593
Citrus sinensis	scaffold00167	3	CH_csi_182	9	13	0.000170101
Eucalyptus grandis	scaffold_1	1	CH_egr_589	5	5	0.00044222
Eucalyptus grandis	scaffold_10	1	CH_egr_123	13	15	0.0000000000000099772
Eucalyptus grandis	scaffold_6	1	CH_egr_590	5	5	0.00044222
Eucalyptus grandis	scaffold_7	1	CH_egr_126	17	32	0.0000000000000179905
Eucalyptus grandis	scaffold_10	2	CH_egr_209	13	15	0.00000000000382234
Eucalyptus grandis	scaffold_7	2	CH_egr_238	17	32	0.0000000000361807
Eucalyptus grandis	scaffold_7	3	CH_egr_544	9	11	0.0000017221
Eucalyptus grandis	scaffold_10	4	CH_egr_95	13	15	0.0000000000000099772
Eucalyptus grandis	scaffold_7	4	CH_egr_96	17	32	0.0000000000000179905
Eucalyptus grandis	scaffold_10	5	CH_egr_120	13	15	0.00000000000382234
Eucalyptus grandis	scaffold_7	5	CH_egr_125	17	32	0.0000000000361807
Fragaria vesca	LG7	1	CH_fve_215	6	8	0.000211771
Fragaria vesca	LG3	3	CH_fve_279	7	8	0.0000652478
Fragaria vesca	LG5	3	CH_fve_352	7	9	0.000282704
Fragaria vesca	LG7	5	CH_fve_70	22	139	0.00050947
Fragaria vesca	LG7	6	CH_fve_92	24	140	0.000200357
Glycine max	Gm20	1	CH_gma_347	6	6	0.000613654
Gossypium raimondii	Chr06	1	CH_gra_256	11	25	0.000374029
Gossypium raimondii	Chr12	3	CH_gra_58	19	23	0.0000000000000235295
Gossypium raimondii	Chr06	4	CH_gra_75	11	25	0.000374029
Gossypium raimondii	Chr01	5	CH_gra_71	13	26	0.0000865411
Gossypium raimondii	Chr01	6	CH_gra_77	14	27	0.0000186883
Gossypium raimondii	Chr12	6	CH_gra_40	19	23	0.0000000000000235295
Malus domestica	1	1	CH_mdo_62	10	21	0.000000297618
Malus domestica	7	1	CH_mdo_140	7	12	0.0000737388
Malus domestica	1	2	CH_mdo_89	10	17	0.00000142965
Malus domestica	7	3	CH_mdo_146	9	13	0.00000492157
Malus domestica	1	4	CH_mdo_12	10	21	0.000000297618
Malus domestica	1	5	CH_mdo_17	10	17	0.00000142965
Medicago truncatula	chr3	1	CH_mtr_412	8	20	0.000077193
Medicago truncatula	chr5	1	CH_mtr_563	5	6	0.000748569
Medicago truncatula	chr1	3	CH_mtr_149	13	18	0.00000000000967882
Medicago truncatula	chr3	3	CH_mtr_365	8	9	0.000000434774
Medicago truncatula	chr3	3	CH_mtr_767	15	73	0.000329416
Medicago truncatula	chr1	6	CH_mtr_89	13	18	0.00000000000967882
Medicago truncatula	chr3	6	CH_mtr_248	15	73	0.000329416
Oryza sativa ssp. japonica	11	1	CH_osa_311	5	5	0.000210077
Oryza sativa ssp. japonica	11	2	CH_osa_411	5	5	0.000764313
Oryza sativa ssp. japonica	4	3	CH_osa_410	6	7	0.000227647
Populus trichocarpa	Chr02	1	CH_ptr_377	7	10	0.000951041
Populus trichocarpa	Chr03	1	CH_ptr_139	22	80	0.0000000429524
Populus trichocarpa	Chr04	1	CH_ptr_59	16	21	0.0000000000000544775
Populus trichocarpa	Chr15	1	CH_ptr_248	10	19	0.0000417132
Populus trichocarpa	Chr02	2	CH_ptr_424	8	11	0.000650742
Populus trichocarpa	Chr03	2	CH_ptr_265	22	80	0.0000186517
Populus trichocarpa	Chr15	2	CH_ptr_423	8	11	0.000650742
Populus trichocarpa	Chr02	3	CH_ptr_564	8	11	0.000882272
Populus trichocarpa	Chr03	3	CH_ptr_120	29	80	0.000000000026839
Populus trichocarpa	Chr03	4	CH_ptr_66	22	80	0.0000000429524
Populus trichocarpa	Chr04	4	CH_ptr_42	16	21	0.0000000000000544775
Populus trichocarpa	Chr15	4	CH_ptr_96	10	19	0.0000417132
Populus trichocarpa	Chr03	5	CH_ptr_92	22	80	0.0000186517
Populus trichocarpa	Chr15	5	CH_ptr_118	10	19	0.000860288
Populus trichocarpa	Chr03	6	CH_ptr_70	29	80	0.000000000026839
Prunus persica	scaffold_2	1	CH_ppe_73	14	22	0.0000000000682818
Prunus persica	scaffold_4	1	CH_ppe_190	7	7	0.00000286701
Prunus persica	scaffold_7	1	CH_ppe_79	10	10	0.000000000148513
Prunus persica	scaffold_4	2	CH_ppe_261	7	7	0.0000302806
Prunus persica	scaffold_7	2	CH_ppe_118	10	10	0.00000000432557
Prunus persica	scaffold_4	3	CH_ppe_322	7	7	0.0000390795
Prunus persica	scaffold_7	3	CH_ppe_144	10	10	0.00000000622969
Prunus persica	scaffold_2	4	CH_ppe_47	14	22	0.0000000000682818
Prunus persica	scaffold_7	4	CH_ppe_48	10	10	0.000000000148513
Prunus persica	scaffold_7	5	CH_ppe_55	10	10	0.00000000432557
Prunus persica	scaffold_2	6	CH_ppe_69	40	186	0.00000000162071
Prunus persica	scaffold_7	6	CH_ppe_73	10	10	0.00000000622969
Ricinus communis	30076	1	CH_rco_143	10	20	0.0000949714
Ricinus communis	30076	4	CH_rco_29	10	20	0.0000949714
Ricinus communis	30076	6	CH_rco_49	10	16	0.0000903226
Solanum lycopersicum	ch08	1	CH_sly_166	9	10	0.000000178982
Solanum lycopersicum	ch08	2	CH_sly_213	9	10	0.00000142198
Solanum lycopersicum	ch08	3	CH_sly_288	9	10	0.00000322053
Solanum lycopersicum	ch08	4	CH_sly_62	10	14	0.00000068548
Solanum lycopersicum	ch08	5	CH_sly_76	10	14	0.0000066511
Solanum lycopersicum	ch08	6	CH_sly_119	10	14	0.0000162622
Solanum tuberosum	chr03	3	CH_stu_752	6	6	0.000647615
Theobroma cacao	scaffold_1	1	CH_tca_287	6	8	0.000518263
Theobroma cacao	scaffold_1	1	CH_tca_173	7	8	0.00000446701
Theobroma cacao	scaffold_10r	1	CH_tca_278	11	40	0.000446624
Theobroma cacao	scaffold_2	1	CH_tca_33	16	27	0.0000000000000361943
Theobroma cacao	scaffold_2	1	CH_tca_65	11	15	0.000000000519806
Theobroma cacao	scaffold_1	2	CH_tca_254	7	8	0.0000954527
Theobroma cacao	scaffold_10r	2	CH_tca_263	16	58	0.000134648
Theobroma cacao	scaffold_2	2	CH_tca_52	15	23	0.0000000000290635
Theobroma cacao	scaffold_1	3	CH_tca_324	7	8	0.00013791
Theobroma cacao	scaffold_10r	3	CH_tca_377	16	58	0.000284144
Theobroma cacao	scaffold_2	3	CH_tca_61	16	23	0.0000000000013883
Theobroma cacao	scaffold_10r	4	CH_tca_76	11	40	0.000446624
Theobroma cacao	scaffold_2	4	CH_tca_21	16	27	0.0000000000000361943
Theobroma cacao	scaffold_2	4	CH_tca_32	11	15	0.000000000519806
Theobroma cacao	scaffold_10r	5	CH_tca_69	16	58	0.000134648
Theobroma cacao	scaffold_2	5	CH_tca_26	15	23	0.0000000000290635
Theobroma cacao	scaffold_2	6	CH_tca_30	16	23	0.0000000000013883
Vitis vinifera	chr15	1	CH_vvi_208	7	10	0.0000335809
Vitis vinifera	chr15	2	CH_vvi_361	7	10	0.000790461
Vitis vinifera	chr4	3	CH_vvi_288	7	7	0.0000165495
Vitis vinifera	chr13_random	4	CH_vvi_64	13	40	0.000000717913
Zea mays	1	1	CH_zma_41	12	19	0.00000000449497
Zea mays	10	1	CH_zma_206	6	7	0.000458647
Zea mays	1	2	CH_zma_58	12	19	0.0000000963475
Zea mays	10	2	CH_zma_161	16	57	0.000101768
Zea mays	4	2	CH_zma_251	9	18	0.000969633
Zea mays	1	3	CH_zma_91	12	19	0.000000324628
Zea mays	10	3	CH_zma_171	19	68	0.0000206549
Zea mays	4	3	CH_zma_219	10	18	0.000110256
Zea mays	1	4	CH_zma_14	12	19	0.00000000449497
Zea mays	1	5	CH_zma_19	12	19	0.0000000963475
Zea mays	1	6	CH_zma_26	12	19	0.000000324628
Zea mays	4	6	CH_zma_40	10	18	0.000110256

Available child term results

GO term	Description	Number of clusters
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	2
GO:0006357	regulation of transcription from RNA polymerase II promoter	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

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