PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Beta vulgaris	mitochondrial	2	CH_bvu_54	12	56	0.00000000313055
Beta vulgaris	mitochondrial	3	CH_bvu_57	13	56	0.000000000206001
Beta vulgaris	mitochondrial	5	CH_bvu_14	12	56	0.00000000313055
Gossypium raimondii	Chr01	4	CH_gra_58	10	78	0.00000299649
Gossypium raimondii	Chr01	10	CH_gra_3	10	78	0.00000130987
Medicago truncatula	chr5	5	CH_mtr_228	10	205	0.000843746
Oryza sativa ssp. japonica	10	1	CH_osa_332	5	13	0.000237047
Oryza sativa ssp. japonica	10	10	CH_osa_17	11	116	0.0000000631827
Oryza sativa ssp. japonica	10	11	CH_osa_20	12	122	0.0000000851099
Oryza sativa ssp. japonica	10	12	CH_osa_22	12	122	0.000000204387
Physcomitrella patens	scaffold_27	2	CH_ppa_53	4	4	0.000271712
Physcomitrella patens	scaffold_27	3	CH_ppa_97	4	4	0.000405485
Physcomitrella patens	scaffold_27	8	CH_ppa_5	4	4	0.000136699
Physcomitrella patens	scaffold_27	9	CH_ppa_7	4	4	0.000206109
Thellungiella parvula	ch3-4	3	CH_tpa_12	13	38	0.0000000000000340223
Thellungiella parvula	ch3-4	6	CH_tpa_5	13	38	0.0000000000000340223
Thellungiella parvula	ch3-4	9	CH_tpa_1	10	34	0.000000000514347
Thellungiella parvula	ch3-4	12	CH_tpa_1	10	34	0.000000000514347
Vitis vinifera	mitochondrial	8	CH_vvi_3	9	70	0.0000503121
Vitis vinifera	mitochondrial	9	CH_vvi_10	9	70	0.000145227

GO term	Description	Number of clusters
GO:0006096	glycolysis	6
GO:0006110	regulation of glycolysis	2
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	1
GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	2
GO:0009060	aerobic respiration	3
GO:0009061	anaerobic respiration	3
GO:0009765	photosynthesis, light harvesting	37
GO:0009769	photosynthesis, light harvesting in photosystem II	20
GO:0009772	photosynthetic electron transport in photosystem II	1
GO:0010205	photoinhibition	2
GO:0010270	photosystem II oxygen evolving complex assembly	2
GO:0010478	chlororespiration	4
GO:0019684	photosynthesis, light reaction	1
GO:0022900	electron transport chain	38
GO:0022904	respiratory electron transport chain	18
GO:0042773	ATP synthesis coupled electron transport	5
GO:0045333	cellular respiration	5

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