PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	1	17	CH_ath_242	3	3	0.00000818379
Arabidopsis thaliana	2	17	CH_ath_272	3	4	0.0000327203
Arabidopsis thaliana	3	17	CH_ath_241	3	3	0.00000818379
Arabidopsis thaliana	3	17	CH_ath_126	4	4	0.00000000462774
Brachypodium distachyon	Bd2	17	CH_bdi_254	3	6	0.00069093
Brachypodium distachyon	Bd3	17	CH_bdi_27	6	7	0.000000000000227903
Chlamydomonas reinhardtii	chromosome_1	17	CH_cre_67	2	2	0.000682555
Chlamydomonas reinhardtii	chromosome_1	19	CH_cre_24	2	2	0.000682555
Oryza sativa ssp. japonica	7	17	CH_osa_187	4	11	0.000000930992
Oryza sativa ssp. japonica	9	17	CH_osa_207	4	13	0.00000201569
Physcomitrella patens	scaffold_102	17	CH_ppa_6	4	9	0.000000111364
Setaria italica	scaffold_6	17	CH_sit_60	9	48	0.000000000000321506
Solanum lycopersicum	ch03	17	CH_sly_118	4	4	0.00000000277678
Vitis vinifera	chr10	17	CH_vvi_172	4	4	0.000000108601
Vitis vinifera	chr11	17	CH_vvi_318	3	3	0.0000793146
Vitis vinifera	chr17	17	CH_vvi_319	3	3	0.0000793146
Vitis vinifera	chr4	17	CH_vvi_35	9	11	1.84915e-20
Vitis vinifera	chr4	17	CH_vvi_435	3	5	0.000791458
Vitis vinifera	chr10	18	CH_vvi_75	10	284	0.000000231397
Zea mays	1	17	CH_zma_68	4	7	0.000000165825
Zea mays	7	17	CH_zma_147	3	5	0.0000809892

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