PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Eucalyptus grandis	scaffold_5	2	CH_egr_636	9	52	0.000103927
Eucalyptus grandis	scaffold_5	3	CH_egr_719	9	52	0.00010651
Prunus persica	scaffold_3	2	CH_ppe_269	9	47	0.0000471892
Prunus persica	scaffold_3	3	CH_ppe_328	9	47	0.0000471892
Ricinus communis	29852	1	CH_rco_38	4	4	0.000000000937579
Solanum lycopersicum	ch01	1	CH_sly_160	4	4	0.000000130496
Solanum lycopersicum	ch07	1	CH_sly_301	3	3	0.000096781
Solanum lycopersicum	ch09	1	CH_sly_206	4	6	0.0000019532
Solanum lycopersicum	ch12	1	CH_sly_31	9	12	9.15125e-20
Solanum lycopersicum	ch12	4	CH_sly_35	11	68	8.13442e-16
Solanum tuberosum	chr10	1	CH_stu_294	3	3	0.00000554258
Theobroma cacao	scaffold_4	2	CH_tca_339	9	58	0.000550979
Theobroma cacao	scaffold_4	3	CH_tca_411	9	58	0.000550979

GO term	Description	Number of clusters
GO:0009512	cytochrome b6f complex	2
GO:0009521	photosystem	12
GO:0009522	photosystem I	16
GO:0009523	photosystem II	9
GO:0009535	chloroplast thylakoid membrane	54
GO:0009538	photosystem I reaction center	3
GO:0009543	chloroplast thylakoid lumen	1
GO:0009654	photosystem II oxygen evolving complex	10
GO:0009783	photosystem II antenna complex	2
GO:0030095	chloroplast photosystem II	1
GO:0042651	thylakoid membrane	2
GO:0044436	thylakoid part	111

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