PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_2	3	CH_aly_196	28	77	0.00000628374
Arabidopsis lyrata	scaffold_2	6	CH_aly_45	30	85	0.00000337968
Carica papaya	supercontig_27	3	CH_cpa_28	25	42	0.0000000000141211
Carica papaya	supercontig_27	6	CH_cpa_12	25	42	0.0000000000141211
Glycine max	Gm06	6	CH_gma_10	81	137	7.61656e-37
Gossypium raimondii	Chr02	4	CH_gra_78	10	13	0.00051469
Gossypium raimondii	Chr02	5	CH_gra_84	10	13	0.000616419
Oryza sativa ssp. japonica	4	1	CH_osa_333	19	65	0.00024066
Oryza sativa ssp. japonica	4	2	CH_osa_357	19	65	0.000305229
Oryza sativa ssp. japonica	4	4	CH_osa_79	36	167	0.00000076087
Oryza sativa ssp. japonica	4	5	CH_osa_91	36	167	0.00000114682
Theobroma cacao	scaffold_2	4	CH_tca_40	16	24	0.0000000540816
Theobroma cacao	scaffold_2	5	CH_tca_43	16	24	0.000000074385
Vitis vinifera	chr18	3	CH_vvi_250	30	71	0.00000452302

GO term	Description	Number of clusters
GO:0005524	ATP binding	54
GO:0005525	GTP binding	29
GO:0010181	FMN binding	71
GO:0016208	AMP binding	3
GO:0030553	cGMP binding	3
GO:0032555	purine ribonucleotide binding	30
GO:0032559	adenyl ribonucleotide binding	76
GO:0043531	ADP binding	1129

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