PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Eucalyptus grandis	scaffold_5	6	CH_egr_171	14	126	0.00000000068295
Glycine max	Gm19	4	CH_gma_65	10	191	0.000120788
Medicago truncatula	chr1	4	CH_mtr_156	10	251	0.000028332
Medicago truncatula	chr7	4	CH_mtr_85	13	235	0.000000000954611
Medicago truncatula	chr4	6	CH_mtr_163	14	276	0.00000380412
Solanum lycopersicum	ch02	3	CH_sly_563	4	5	0.000426392
Solanum tuberosum	chr02	3	CH_stu_450	5	6	0.00000447642
Solanum tuberosum	chr07	3	CH_stu_584	4	4	0.000102998

GO term	Description	Number of clusters
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:0010215	cellulose microfibril organization	32
GO:0010246	rhamnogalacturonan I biosynthetic process	4
GO:0042545	cell wall modification	66
GO:0052541	plant-type cell wall cellulose metabolic process	2
GO:0071668	plant-type cell wall assembly	8

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