PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0003677
Description: DNA binding

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_1	1	CH_aly_167	9	13	0.0000955675
Arabidopsis lyrata	scaffold_1	2	CH_aly_237	9	13	0.000177551
Arabidopsis lyrata	scaffold_1	3	CH_aly_343	9	13	0.000391698
Brassica rapa	A10	1	CH_bra_52	13	18	0.00000014944
Brassica rapa	A10	2	CH_bra_80	13	18	0.000000375013
Brassica rapa	A10	4	CH_bra_10	13	18	0.00000014944
Brassica rapa	A10	5	CH_bra_19	13	18	0.000000375013
Capsella rubella	scaffold_1	1	CH_cru_202	8	10	0.000368166
Capsella rubella	scaffold_1	2	CH_cru_318	8	10	0.000660693
Eucalyptus grandis	scaffold_4	1	CH_egr_409	9	12	0.00000589968
Eucalyptus grandis	scaffold_5	1	CH_egr_280	11	14	0.0000000203026
Eucalyptus grandis	scaffold_7	1	CH_egr_593	7	9	0.000482893
Eucalyptus grandis	scaffold_9	1	CH_egr_523	7	8	0.000111783
Eucalyptus grandis	scaffold_4	2	CH_egr_532	9	12	0.0000113442
Eucalyptus grandis	scaffold_7	2	CH_egr_574	8	10	0.0000493953
Eucalyptus grandis	scaffold_9	2	CH_egr_687	7	8	0.000186651
Eucalyptus grandis	scaffold_4	3	CH_egr_631	9	12	0.0000302823
Eucalyptus grandis	scaffold_9	3	CH_egr_825	7	8	0.000403389
Eucalyptus grandis	scaffold_4	4	CH_egr_209	10	18	0.000043315
Eucalyptus grandis	scaffold_5	4	CH_egr_147	11	14	0.0000000203026
Eucalyptus grandis	scaffold_5	4	CH_egr_157	24	93	0.00000011416
Eucalyptus grandis	scaffold_4	5	CH_egr_254	10	18	0.0000881979
Fragaria vesca	LG5	1	CH_fve_247	7	9	0.000522478
Fragaria vesca	LG5	2	CH_fve_342	7	9	0.000870077
Fragaria vesca	LG7	2	CH_fve_303	12	31	0.000473377
Fragaria vesca	LG7	5	CH_fve_67	12	31	0.000473377
Gossypium raimondii	Chr03	1	CH_gra_100	12	14	0.000000022722
Gossypium raimondii	Chr12	1	CH_gra_129	13	20	0.000000934696
Gossypium raimondii	Chr03	2	CH_gra_121	12	14	0.0000000475508
Gossypium raimondii	Chr12	2	CH_gra_156	13	20	0.00000203834
Gossypium raimondii	Chr03	3	CH_gra_151	12	14	0.000000142938
Gossypium raimondii	Chr03	4	CH_gra_50	12	14	0.000000022722
Gossypium raimondii	Chr12	4	CH_gra_54	13	20	0.000000934696
Gossypium raimondii	Chr03	5	CH_gra_52	12	14	0.0000000475508
Gossypium raimondii	Chr12	5	CH_gra_60	13	20	0.00000203834
Gossypium raimondii	Chr03	6	CH_gra_62	12	14	0.000000142938
Malus domestica	7	2	CH_mdo_205	8	13	0.000248887
Manihot esculenta	scaffold06914	3	CH_mes_26	15	17	0.0000000000647901
Manihot esculenta	scaffold06914	6	CH_mes_10	15	17	0.0000000000647901
Medicago truncatula	chr1	1	CH_mtr_125	15	28	0.0000000000695162
Medicago truncatula	chr3	1	CH_mtr_271	8	9	0.000000674887
Medicago truncatula	chr6	1	CH_mtr_333	10	19	0.00000566846
Medicago truncatula	chr1	2	CH_mtr_151	15	28	0.000000000172301
Medicago truncatula	chr3	2	CH_mtr_334	8	9	0.00000110745
Medicago truncatula	chr6	2	CH_mtr_398	10	19	0.0000103732
Medicago truncatula	chr1	3	CH_mtr_230	15	28	0.00000000204192
Medicago truncatula	chr6	3	CH_mtr_577	10	19	0.0000538106
Medicago truncatula	chr1	4	CH_mtr_75	15	28	0.0000000000695162
Medicago truncatula	chr6	4	CH_mtr_136	10	19	0.00000566846
Medicago truncatula	chr1	5	CH_mtr_78	15	28	0.000000000172301
Medicago truncatula	chr6	5	CH_mtr_146	10	19	0.0000103732
Medicago truncatula	chr1	6	CH_mtr_106	15	28	0.00000000204192
Medicago truncatula	chr6	6	CH_mtr_198	10	19	0.0000538106
Oryza sativa ssp. japonica	12	1	CH_osa_258	7	8	0.0000421973
Oryza sativa ssp. japonica	12	2	CH_osa_274	7	8	0.0000566719
Oryza sativa ssp. japonica	12	3	CH_osa_371	7	8	0.000126727
Oryza sativa ssp. japonica	5	4	CH_osa_136	28	205	0.000190752
Oryza sativa ssp. japonica	5	5	CH_osa_162	28	205	0.00047343
Oryza sativa ssp. japonica	4	6	CH_osa_141	10	18	0.0000426912
Physcomitrella patens	scaffold_259	4	CH_ppa_7	10	26	0.000802649
Populus trichocarpa	Chr03	2	CH_ptr_246	8	8	0.0000092236
Populus trichocarpa	Chr04	2	CH_ptr_89	17	22	0.00000000000250034
Populus trichocarpa	Chr04	3	CH_ptr_69	19	22	0.0000000000000044564
Populus trichocarpa	Chr04	5	CH_ptr_50	17	22	0.00000000000250034
Populus trichocarpa	Chr04	6	CH_ptr_50	19	22	0.0000000000000044564
Prunus persica	scaffold_1	1	CH_ppe_327	6	6	0.000875273
Prunus persica	scaffold_2	2	CH_ppe_104	17	29	0.00000000115357
Prunus persica	scaffold_2	5	CH_ppe_49	17	29	0.00000000115357
Ricinus communis	30076	2	CH_rco_230	10	20	0.000657399
Ricinus communis	30076	5	CH_rco_38	10	20	0.000657399
Solanum tuberosum	chr08	1	CH_stu_103	15	17	0.000000000000620545
Solanum tuberosum	chr08	2	CH_stu_122	15	17	0.00000000000168257
Solanum tuberosum	chr08	3	CH_stu_187	15	17	0.0000000000184573
Solanum tuberosum	chr08	4	CH_stu_66	15	17	0.000000000000620545
Solanum tuberosum	chr08	5	CH_stu_68	15	17	0.00000000000168257
Solanum tuberosum	chr08	6	CH_stu_97	15	17	0.0000000000184573
Theobroma cacao	scaffold_2	2	CH_tca_54	24	60	0.000000000039626
Theobroma cacao	scaffold_2	3	CH_tca_25	30	56	3.0069e-18
Theobroma cacao	scaffold_2	5	CH_tca_27	24	60	0.000000000039626
Theobroma cacao	scaffold_2	6	CH_tca_18	31	60	2.49383e-18
Vitis vinifera	chr2	4	CH_vvi_87	12	28	0.000059536
Vitis vinifera	chr2	5	CH_vvi_91	12	28	0.000155431
Vitis vinifera	chr2	6	CH_vvi_133	12	28	0.000641862
Zea mays	10	2	CH_zma_227	18	65	0.000505779
Zea mays	10	4	CH_zma_32	23	102	0.000139524

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:0003684	damaged DNA binding	4
GO:0003689	DNA clamp loader activity	5
GO:0008327	methyl-CpG binding	1
GO:0030983	mismatched DNA binding	1
GO:0043565	sequence-specific DNA binding	40
GO:0080084	5S rDNA binding	4
GO:0097100	supercoiled DNA binding	10

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