PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0003676
Description: nucleic acid binding

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_8	4	CH_aly_31	58	270	0.0000726069
Arabidopsis lyrata	scaffold_8	5	CH_aly_53	60	270	0.0000598008
Arabidopsis thaliana	2	7	CH_ath_30	23	57	0.000324496
Arabidopsis thaliana	2	8	CH_ath_29	23	57	0.000353173
Arabidopsis thaliana	2	9	CH_ath_39	23	57	0.000853262
Arabidopsis thaliana	2	10	CH_ath_38	23	57	0.000324496
Arabidopsis thaliana	2	11	CH_ath_38	23	57	0.000353173
Arabidopsis thaliana	2	12	CH_ath_45	23	57	0.000853262
Brassica rapa	A02	6	CH_bra_50	33	96	0.000850808
Capsella rubella	scaffold_8	5	CH_cru_83	61	265	0.000992736
Capsella rubella	scaffold_6	6	CH_cru_107	11	14	0.00062148
Fragaria vesca	LG5	3	CH_fve_302	30	77	0.000148409
Fragaria vesca	LG5	4	CH_fve_57	34	128	0.000294193
Fragaria vesca	LG5	5	CH_fve_78	34	128	0.000998038
Fragaria vesca	LG5	6	CH_fve_63	44	128	0.0000053325
Lotus japonicus	chr3	6	CH_lja_27	17	43	0.000264095
Medicago truncatula	chr3	1	CH_mtr_284	10	13	0.00000143315
Medicago truncatula	chr3	2	CH_mtr_356	10	13	0.00000242584
Medicago truncatula	chr3	3	CH_mtr_589	10	13	0.0000612834
Medicago truncatula	chr3	4	CH_mtr_120	10	13	0.00000143315
Medicago truncatula	chr3	5	CH_mtr_132	10	13	0.00000242584
Medicago truncatula	chr3	6	CH_mtr_201	10	13	0.0000612834
Oryza sativa ssp. japonica	4	1	CH_osa_309	21	36	0.000207883
Oryza sativa ssp. japonica	4	2	CH_osa_352	21	36	0.000263212
Oryza sativa ssp. japonica	4	3	CH_osa_366	19	28	0.000116004
Oryza sativa ssp. japonica	5	3	CH_osa_481	27	54	0.000786293
Oryza sativa ssp. japonica	3	4	CH_osa_87	87	281	0.00000139745
Oryza sativa ssp. japonica	4	4	CH_osa_39	106	299	0.000000000000310836
Oryza sativa ssp. japonica	5	4	CH_osa_44	103	295	0.00000000000303716
Oryza sativa ssp. japonica	7	4	CH_osa_94	47	117	0.00000356139
Oryza sativa ssp. japonica	3	5	CH_osa_98	87	281	0.00000274878
Oryza sativa ssp. japonica	4	5	CH_osa_42	106	299	0.000000000000781436
Oryza sativa ssp. japonica	5	5	CH_osa_46	103	295	0.00000000000736364
Oryza sativa ssp. japonica	7	5	CH_osa_102	47	117	0.00000555827
Oryza sativa ssp. japonica	4	6	CH_osa_45	114	299	0.000000000000014294
Oryza sativa ssp. japonica	7	6	CH_osa_105	50	117	0.00000115825
Oryza sativa ssp. japonica	8	6	CH_osa_161	86	283	0.000291515
Oryza sativa ssp. japonica	10	7	CH_osa_40	30	68	0.000295446
Oryza sativa ssp. japonica	10	8	CH_osa_45	30	68	0.000401448
Oryza sativa ssp. japonica	4	9	CH_osa_49	17	25	0.000454146
Oryza sativa ssp. japonica	3	10	CH_osa_23	89	304	0.0000029825
Oryza sativa ssp. japonica	4	10	CH_osa_21	90	316	0.00000147023
Oryza sativa ssp. japonica	4	10	CH_osa_58	83	317	0.000489928
Oryza sativa ssp. japonica	7	10	CH_osa_20	47	117	0.00000123898
Oryza sativa ssp. japonica	3	11	CH_osa_33	89	304	0.00000589953
Oryza sativa ssp. japonica	4	11	CH_osa_30	90	316	0.00000294581
Oryza sativa ssp. japonica	4	11	CH_osa_73	83	317	0.00088556
Oryza sativa ssp. japonica	7	11	CH_osa_29	47	117	0.00000195195
Oryza sativa ssp. japonica	8	11	CH_osa_36	58	172	0.00000742744
Oryza sativa ssp. japonica	10	12	CH_osa_34	80	253	0.0000029848
Oryza sativa ssp. japonica	3	12	CH_osa_47	91	305	0.0000206864
Oryza sativa ssp. japonica	4	12	CH_osa_29	94	316	0.00000152077
Oryza sativa ssp. japonica	7	12	CH_osa_23	50	117	0.000000218565
Oryza sativa ssp. japonica	8	12	CH_osa_46	59	172	0.0000200368
Ostreococcus lucimarinus	Chr_2	1	CH_olu_3	17	21	0.00000000370455
Ostreococcus lucimarinus	Chr_2	4	CH_olu_2	17	21	0.00000000370455
Populus trichocarpa	Chr16	1	CH_ptr_164	30	80	0.000000422331
Populus trichocarpa	Chr16	2	CH_ptr_216	30	80	0.00000177765
Populus trichocarpa	Chr16	3	CH_ptr_298	30	73	0.00000380831
Populus trichocarpa	Chr16	4	CH_ptr_70	31	83	0.000000217428
Populus trichocarpa	Chr16	5	CH_ptr_78	31	83	0.000000958048
Populus trichocarpa	Chr16	6	CH_ptr_93	39	103	0.000000135711
Prunus persica	scaffold_6	5	CH_ppe_121	61	252	0.000374189
Prunus persica	scaffold_6	6	CH_ppe_147	69	260	0.000419597
Solanum tuberosum	chr06	3	CH_stu_474	20	34	0.0000112118
Solanum tuberosum	chr06	6	CH_stu_154	55	175	0.00000367602
Theobroma cacao	scaffold_2	6	CH_tca_114	84	294	0.000282999
Theobroma cacao	scaffold_3	6	CH_tca_120	52	154	0.000509473
Theobroma cacao	scaffold_4	6	CH_tca_101	80	271	0.000126118
Theobroma cacao	scaffold_5	6	CH_tca_74	91	298	0.00000156953
Theobroma cacao	scaffold_6	6	CH_tca_72	46	109	0.000000748003
Theobroma cacao	scaffold_9	6	CH_tca_90	58	169	0.0000392747
Vitis vinifera	chr15	4	CH_vvi_104	10	15	0.000605844

Available child term results

GO term	Description	Number of clusters
GO:0000049	tRNA binding	2
GO:0000499	base pairing with mRNA	57
GO:0000976	transcription regulatory region sequence-specific DNA binding	3
GO:0001164	RNA polymerase I CORE element sequence-specific DNA binding	1
GO:0003677	DNA binding	85
GO:0003684	damaged DNA binding	4
GO:0003689	DNA clamp loader activity	5
GO:0003723	RNA binding	22
GO:0003725	double-stranded RNA binding	5
GO:0003729	mRNA binding	1
GO:0003730	mRNA 3'-UTR binding	12
GO:0003746	translation elongation factor activity	47
GO:0003747	translation release factor activity	1
GO:0008097	5S rRNA binding	7
GO:0008143	poly(A) RNA binding	4
GO:0008312	7S RNA binding	1
GO:0008327	methyl-CpG binding	1
GO:0016149	translation release factor activity, codon specific	7
GO:0017069	snRNA binding	9
GO:0017070	U6 snRNA binding	3
GO:0019843	rRNA binding	12
GO:0030619	U1 snRNA binding	4
GO:0030983	mismatched DNA binding	1
GO:0035197	siRNA binding	3
GO:0035198	miRNA binding	4
GO:0043565	sequence-specific DNA binding	40
GO:0080084	5S rDNA binding	4
GO:0097100	supercoiled DNA binding	10
GO:0097157	pre-mRNA intronic binding	6

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