PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	1	CH_ath_281	13	74	0.000181238
Arabidopsis thaliana	5	7	CH_ath_22	13	74	0.0000264191
Arabidopsis thaliana	5	8	CH_ath_23	13	74	0.0000517942
Arabidopsis thaliana	5	9	CH_ath_24	13	74	0.0000769553
Malus domestica	1	3	CH_mdo_81	7	16	0.000000151285
Manihot esculenta	scaffold06948	2	CH_mes_159	4	4	0.000257287
Manihot esculenta	scaffold06948	3	CH_mes_247	4	4	0.000388269
Medicago truncatula	chr4	2	CH_mtr_476	7	38	0.0000735388
Populus trichocarpa	Chr06	5	CH_ptr_96	11	101	0.0000233186
Populus trichocarpa	Chr06	6	CH_ptr_129	11	101	0.000129203
Theobroma cacao	scaffold_9	5	CH_tca_52	10	66	0.00000163711
Zea mays	1	6	CH_zma_43	10	103	0.000187557

GO term	Description	Number of clusters
GO:0009252	peptidoglycan biosynthetic process	5
GO:0009664	plant-type cell wall organization	50
GO:0009827	plant-type cell wall modification	2
GO:0009828	plant-type cell wall loosening	3
GO:0009829	cell wall modification involved in fruit ripening	2
GO:0009830	cell wall modification involved in abscission	10
GO:0009832	plant-type cell wall biogenesis	15
GO:0009834	secondary cell wall biogenesis	2
GO:0010215	cellulose microfibril organization	32
GO:0010246	rhamnogalacturonan I biosynthetic process	4
GO:0010411	xyloglucan metabolic process	8
GO:0016998	cell wall macromolecule catabolic process	29
GO:0042545	cell wall modification	66
GO:0044036	cell wall macromolecule metabolic process	3
GO:0045493	xylan catabolic process	2
GO:0052541	plant-type cell wall cellulose metabolic process	2
GO:0071555	cell wall organization	8
GO:0071668	plant-type cell wall assembly	8
GO:0071669	plant-type cell wall organization or biogenesis	3

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