PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	2	13	CH_ath_352	3	3	0.000048566
Brachypodium distachyon	Bd3	13	CH_bdi_186	4	5	0.00000103348
Brachypodium distachyon	Bd4	13	CH_bdi_101	5	6	0.00000000195476
Brachypodium distachyon	Bd4	13	CH_bdi_159	4	4	0.000000206965
Oryza sativa ssp. indica	Chr08	13	CH_osaindica_861	3	5	0.000482429
Oryza sativa ssp. indica	Chr11	13	CH_osaindica_285	5	10	0.0000000100405
Oryza sativa ssp. indica	Chr12	13	CH_osaindica_743	3	4	0.000193108
Oryza sativa ssp. japonica	11	13	CH_osa_271	5	13	0.0000000266544
Oryza sativa ssp. japonica	12	13	CH_osa_346	4	6	0.000000397295
Oryza sativa ssp. japonica	9	13	CH_osa_153	5	5	0.0000000000208197
Setaria italica	scaffold_1	13	CH_sit_174	6	13	0.0000000009818
Setaria italica	scaffold_2	13	CH_sit_212	5	7	0.00000000794481
Setaria italica	scaffold_5	13	CH_sit_561	4	12	0.000119877
Setaria italica	scaffold_7	13	CH_sit_291	4	5	0.000000244646
Setaria italica	scaffold_8	13	CH_sit_574	3	3	0.000154979
Solanum lycopersicum	ch01	13	CH_sly_566	3	3	0.000129543
Solanum lycopersicum	ch05	13	CH_sly_110	6	6	0.000000000000405626
Sorghum bicolor	chr_2	13	CH_sbi_138	5	5	0.000000000163607
Sorghum bicolor	chr_3	13	CH_sbi_307	6	41	0.000000905689
Sorghum bicolor	chr_4	13	CH_sbi_623	3	4	0.000373482
Vitis vinifera	chr13	13	CH_vvi_331	4	7	0.00000122134
Zea mays	7	13	CH_zma_66	5	5	0.000000000183297

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