PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	3	13	CH_ath_29	8	11	1.01087e-19
Arabidopsis thaliana	5	13	CH_ath_154	4	4	0.0000000067224
Brachypodium distachyon	Bd1	13	CH_bdi_171	4	7	0.00000032415
Brachypodium distachyon	Bd1	13	CH_bdi_74	5	7	0.000000000131461
Brachypodium distachyon	Bd4	13	CH_bdi_299	3	4	0.0000520161
Oryza sativa ssp. indica	Chr07	13	CH_osaindica_319	4	6	0.0000000314577
Oryza sativa ssp. indica	Chr07	13	CH_osaindica_356	4	8	0.000000146704
Oryza sativa ssp. japonica	12	13	CH_osa_519	3	4	0.0000279037
Oryza sativa ssp. japonica	12	13	CH_osa_258	6	53	0.0000000139502
Oryza sativa ssp. japonica	7	13	CH_osa_312	4	7	0.000000113174
Populus trichocarpa	Chr07	13	CH_ptr_266	5	14	0.0000000156168
Setaria italica	scaffold_2	13	CH_sit_340	4	9	0.00000118541
Setaria italica	scaffold_2	13	CH_sit_219	4	4	0.00000000943375
Setaria italica	scaffold_3	13	CH_sit_432	3	3	0.0000139443
Setaria italica	scaffold_4	13	CH_sit_638	3	6	0.000278437
Solanum lycopersicum	ch03	13	CH_sly_163	5	10	0.000000000316956
Sorghum bicolor	chr_2	13	CH_sbi_196	4	4	0.00000000627025
Sorghum bicolor	chr_9	13	CH_sbi_390	3	3	0.000010268
Vitis vinifera	chr14	13	CH_vvi_143	5	7	0.0000000000585579

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