PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_7	4	CH_aly_34	10	125	0.000119273
Cucumis melo	CM3.5_scaffold00007	3	CH_cme_252	4	4	0.000116493
Glycine max	Gm16	1	CH_gma_307	4	5	0.000336636
Medicago truncatula	chr1	1	CH_mtr_372	4	5	0.0000273905
Medicago truncatula	chr1	2	CH_mtr_534	4	5	0.000150553
Medicago truncatula	chr1	3	CH_mtr_717	4	5	0.00026204
Medicago truncatula	chr1	4	CH_mtr_151	10	184	0.0000219315
Oryza sativa ssp. japonica	10	1	CH_osa_361	4	8	0.000486096
Oryza sativa ssp. japonica	5	1	CH_osa_163	5	7	0.000000483819
Oryza sativa ssp. japonica	1	2	CH_osa_58	11	40	0.00000000000190482
Oryza sativa ssp. japonica	5	2	CH_osa_179	5	7	0.00000236735
Prunus persica	scaffold_7	1	CH_ppe_78	7	9	0.000000000121618
Prunus persica	scaffold_7	2	CH_ppe_108	7	9	0.00000000182214
Prunus persica	scaffold_7	3	CH_ppe_138	7	9	0.0000000031717
Solanum lycopersicum	ch10	4	CH_sly_67	12	92	0.00000236401
Solanum lycopersicum	ch10	5	CH_sly_81	12	92	0.0000124766
Solanum lycopersicum	ch10	6	CH_sly_124	12	92	0.000034115

GO term	Description	Number of clusters
GO:0004326	tetrahydrofolylpolyglutamate synthase activity	6
GO:0004357	glutamate-cysteine ligase activity	7
GO:0004363	glutathione synthase activity	16
GO:0004632	phosphopantothenate--cysteine ligase activity	1
GO:0004639	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity	3
GO:0004842	ubiquitin-protein ligase activity	15
GO:0008716	D-alanine-D-alanine ligase activity	6
GO:0008841	dihydrofolate synthase activity	2
GO:0010279	indole-3-acetic acid amido synthetase activity	3
GO:0034450	ubiquitin-ubiquitin ligase activity	3
GO:0080123	jasmonate-amino synthetase activity	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