PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	1	13	CH_ath_334	7	20	0.0000278997
Arabidopsis thaliana	5	13	CH_ath_586	5	10	0.000939226
Carica papaya	supercontig_3	13	CH_cpa_158	5	6	0.00000756143
Musa acuminata	chr4	13	CH_mac_398	8	38	0.00052629
Oryza sativa ssp. indica	Chr11	13	CH_osaindica_989	6	20	0.000857474
Oryza sativa ssp. indica	Chr11	14	CH_osaindica_117	11	114	0.000335691
Oryza sativa ssp. japonica	11	13	CH_osa_315	8	21	0.000000151663
Oryza sativa ssp. japonica	11	14	CH_osa_112	12	103	0.00000235148
Oryza sativa ssp. japonica	11	15	CH_osa_14	8	21	0.0000000113316
Oryza sativa ssp. japonica	11	16	CH_osa_27	10	96	0.0000134753
Populus trichocarpa	Chr04	13	CH_ptr_39	25	52	3.01652e-26
Populus trichocarpa	Chr04	14	CH_ptr_39	25	52	3.01652e-26
Setaria italica	scaffold_8	13	CH_sit_742	6	16	0.000654038
Setaria italica	scaffold_8	14	CH_sit_73	12	104	0.000137228
Vitis vinifera	chr10	13	CH_vvi_568	6	12	0.000246442
Vitis vinifera	chrUn	13	CH_vvi_586	10	58	0.000368081
Vitis vinifera	chrUn	14	CH_vvi_85	22	292	0.0000180161
Vitis vinifera	chr19	15	CH_vvi_23	8	30	0.0000229377

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