PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0000166
Description: nucleotide binding

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00071	1	CH_atr_120	21	53	0.00000974841
Amborella trichopoda	scaffold00071	2	CH_atr_126	21	53	0.0000141677
Amborella trichopoda	scaffold00071	3	CH_atr_333	21	53	0.000623728
Amborella trichopoda	scaffold00071	4	CH_atr_37	21	53	0.00000974841
Amborella trichopoda	scaffold00071	5	CH_atr_41	21	53	0.0000141677
Amborella trichopoda	scaffold00071	6	CH_atr_86	21	53	0.000623728
Arabidopsis thaliana	3	3	CH_ath_357	14	22	0.000251477
Arabidopsis thaliana	3	12	CH_ath_43	58	316	0.000549508
Cucumis melo	CM3.5_scaffold00051	4	CH_cme_29	12	17	0.0000171553
Eucalyptus grandis	scaffold_15	3	CH_egr_830	19	30	0.000424762
Eucalyptus grandis	scaffold_10	4	CH_egr_120	83	243	0.0000000000362657
Eucalyptus grandis	scaffold_10	5	CH_egr_130	83	243	0.0000000000777745
Eucalyptus grandis	scaffold_15	6	CH_egr_305	19	30	0.000424762
Glycine max	Gm09	1	CH_gma_126	23	39	0.000000186185
Glycine max	Gm09	2	CH_gma_156	23	39	0.000000253297
Glycine max	Gm05	3	CH_gma_403	21	39	0.000217022
Glycine max	Gm09	3	CH_gma_178	25	41	0.000000165519
Glycine max	Gm09	4	CH_gma_42	23	39	0.000000186185
Glycine max	Gm09	5	CH_gma_50	23	39	0.000000253297
Glycine max	Gm05	6	CH_gma_99	21	39	0.000217022
Glycine max	Gm09	6	CH_gma_62	25	41	0.000000165519
Lotus japonicus	chr3	1	CH_lja_56	8	9	0.00000893254
Lotus japonicus	chr3	2	CH_lja_77	8	9	0.0000115404
Lotus japonicus	chr3	3	CH_lja_114	8	9	0.0000609997
Medicago truncatula	chr7	5	CH_mtr_210	23	81	0.000417605
Oryza sativa ssp. japonica	4	3	CH_osa_308	23	65	0.0000424349
Oryza sativa ssp. japonica	1	4	CH_osa_108	14	26	0.0000167694
Oryza sativa ssp. japonica	1	5	CH_osa_120	14	26	0.0000197385
Oryza sativa ssp. japonica	1	6	CH_osa_121	15	26	0.00000913166
Oryza sativa ssp. japonica	4	6	CH_osa_100	43	167	0.000000559364
Prunus persica	scaffold_1	4	CH_ppe_101	32	93	0.000174905
Ricinus communis	30146	6	CH_rco_39	52	168	0.0000076567
Solanum tuberosum	chr11	3	CH_stu_96	27	29	3.43791e-16
Vitis vinifera	chr10	2	CH_vvi_267	29	78	0.000118074
Vitis vinifera	chr10	3	CH_vvi_318	27	56	0.0000517227
Vitis vinifera	chr10	5	CH_vvi_90	29	78	0.000118074
Vitis vinifera	chr10	6	CH_vvi_100	34	78	0.0000131314
Zea mays	10	6	CH_zma_33	12	15	0.0000408303

Available child term results

GO term	Description	Number of clusters
GO:0000774	adenyl-nucleotide exchange factor activity	4
GO:0005524	ATP binding	54
GO:0005525	GTP binding	29
GO:0008327	methyl-CpG binding	1
GO:0010181	FMN binding	71
GO:0016208	AMP binding	3
GO:0017076	purine nucleotide binding	9
GO:0030553	cGMP binding	3
GO:0030554	adenyl nucleotide binding	12
GO:0032553	ribonucleotide binding	14
GO:0032555	purine ribonucleotide binding	30
GO:0032559	adenyl ribonucleotide binding	76
GO:0043531	ADP binding	1129
GO:0050660	flavin adenine dinucleotide binding	43
GO:0050661	NADP binding	7
GO:0051287	NAD binding	53
GO:0070401	NADP+ binding	25
GO:0070403	NAD+ 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