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_277	4	5	0.0000358214
Arabidopsis thaliana	1	17	CH_ath_312	4	6	0.000107139
Arabidopsis thaliana	2	17	CH_ath_94	7	9	0.0000000000132355
Brachypodium distachyon	Bd4	17	CH_bdi_100	5	6	0.000000431358
Oryza sativa ssp. japonica	10	17	CH_osa_227	6	13	0.00000452174
Oryza sativa ssp. japonica	11	17	CH_osa_392	8	66	0.000411915
Oryza sativa ssp. japonica	12	17	CH_osa_183	10	68	0.00000073222
Oryza sativa ssp. japonica	9	17	CH_osa_175	5	5	0.000000455033
Oryza sativa ssp. japonica	12	18	CH_osa_66	10	68	0.00000073222
Populus trichocarpa	Chr11	17	CH_ptr_394	4	4	0.000224992
Populus trichocarpa	Chr11	17	CH_ptr_136	7	8	0.00000000112548
Setaria italica	scaffold_1	17	CH_sit_267	4	4	0.0000142883
Setaria italica	scaffold_2	17	CH_sit_110	6	7	0.00000000192854
Setaria italica	scaffold_4	17	CH_sit_456	4	8	0.000986018
Solanum lycopersicum	ch01	17	CH_sly_385	4	4	0.000239618
Solanum lycopersicum	ch03	17	CH_sly_90	7	7	0.000000000175508
Solanum lycopersicum	ch05	17	CH_sly_91	7	7	0.000000000175508
Vitis vinifera	chr10	17	CH_vvi_276	4	4	0.0000180015
Vitis vinifera	chr11	17	CH_vvi_262	5	9	0.0000111983
Vitis vinifera	chr12	17	CH_vvi_170	5	5	0.0000000903807
Vitis vinifera	chr16	17	CH_vvi_322	4	5	0.0000896426
Vitis vinifera	chr4	17	CH_vvi_198	5	6	0.000000540012
Vitis vinifera	chr8	17	CH_vvi_60	11	24	0.00000000000000290506
Vitis vinifera	chr8	18	CH_vvi_43	11	24	0.00000000000000290506
Zea mays	7	17	CH_zma_47	5	5	0.0000000270385

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