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_520	3	4	0.000442181
Brachypodium distachyon	Bd2	13	CH_bdi_124	6	16	0.0000000137063
Brachypodium distachyon	Bd2	13	CH_bdi_384	3	3	0.000234206
Carica papaya	supercontig_49	13	CH_cpa_47	5	5	0.000000000334509
Carica papaya	supercontig_49	15	CH_cpa_42	3	5	0.000923104
Musa acuminata	chr8	13	CH_mac_328	3	3	0.000175489
Oryza sativa ssp. indica	Chr01	13	CH_osaindica_24	15	56	2.73057e-26
Oryza sativa ssp. indica	Chr03	13	CH_osaindica_713	3	3	0.000142476
Oryza sativa ssp. indica	Chr07	13	CH_osaindica_242	6	15	0.00000000160618
Oryza sativa ssp. indica	Chr01	14	CH_osaindica_22	15	56	2.73057e-26
Oryza sativa ssp. indica	Chr01	15	CH_osaindica_65	5	56	0.00025271
Oryza sativa ssp. japonica	1	13	CH_osa_15	16	54	6.25251e-30
Oryza sativa ssp. japonica	7	13	CH_osa_253	6	22	0.0000000125324
Oryza sativa ssp. japonica	1	14	CH_osa_18	16	54	6.25251e-30
Populus trichocarpa	Chr14	13	CH_ptr_25	16	32	8.48e-31
Populus trichocarpa	Chr14	14	CH_ptr_26	16	32	8.48e-31
Setaria italica	scaffold_5	13	CH_sit_136	7	18	0.0000000000270623
Solanum lycopersicum	ch11	13	CH_sly_558	3	3	0.00010283
Solanum lycopersicum	ch11	15	CH_sly_30	3	3	0.0000749559
Sorghum bicolor	chr_3	13	CH_sbi_78	7	9	0.0000000000000126727
Vitis vinifera	chr6	13	CH_vvi_505	3	3	0.000104717
Vitis vinifera	chr8	13	CH_vvi_131	6	8	0.00000000000922373
Vitis vinifera	chr8	15	CH_vvi_46	3	4	0.000286033
Zea mays	3	13	CH_zma_212	4	6	0.00000278502

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