PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_1	5	CH_aly_79	20	150	0.000623132
Arabidopsis thaliana	4	3	CH_ath_447	16	80	0.000829546
Capsella rubella	scaffold_7	5	CH_cru_57	10	23	0.0000217847
Capsella rubella	scaffold_7	6	CH_cru_74	10	23	0.0000273594
Medicago truncatula	chr4	4	CH_mtr_138	12	220	0.00000677927
Oryza sativa ssp. japonica	7	5	CH_osa_47	10	22	0.00000000000860835
Oryza sativa ssp. japonica	7	6	CH_osa_61	10	22	0.0000000000180065
Populus trichocarpa	Chr09	4	CH_ptr_118	11	219	0.000929719
Populus trichocarpa	Chr09	5	CH_ptr_106	11	94	0.000182684
Populus trichocarpa	Chr09	6	CH_ptr_136	11	94	0.00032393
Solanum lycopersicum	ch10	1	CH_sly_102	9	26	0.000000000735527
Solanum lycopersicum	ch10	2	CH_sly_164	9	26	0.000000130718
Solanum lycopersicum	ch10	8	CH_sly_16	4	5	0.000814222
Solanum tuberosum	chr10	8	CH_stu_17	4	5	0.00092991

GO term	Description	Number of clusters
GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	6
GO:0006032	chitin catabolic process	106
GO:0006308	DNA catabolic process	16
GO:0006511	ubiquitin-dependent protein catabolic process	84
GO:0006515	misfolded or incompletely synthesized protein catabolic process	5
GO:0006516	glycoprotein catabolic process	2
GO:0016075	rRNA catabolic process	1
GO:0016598	protein arginylation	3
GO:0030163	protein catabolic process	2
GO:0030245	cellulose catabolic process	3
GO:0031145	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process	8
GO:0031222	arabinan catabolic process	4
GO:0042176	regulation of protein catabolic process	6
GO:0042177	negative regulation of protein catabolic process	2
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	3
GO:0044257	cellular protein catabolic process	35
GO:0044265	cellular macromolecule catabolic process	2
GO:0045493	xylan catabolic process	2
GO:0051603	proteolysis involved in cellular protein catabolic process	6

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