PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Brachypodium distachyon	Bd1	13	CH_bdi_246	5	16	0.00000909337
Brachypodium distachyon	Bd1	13	CH_bdi_409	3	3	0.000386627
Brachypodium distachyon	Bd3	13	CH_bdi_408	3	3	0.000386627
Brachypodium distachyon	Bd3	13	CH_bdi_211	5	13	0.00000269499
Carica papaya	supercontig_46	13	CH_cpa_298	3	4	0.00011437
Oryza sativa ssp. indica	Chr08	13	CH_osaindica_118	6	6	0.0000000000000684467
Oryza sativa ssp. japonica	8	13	CH_osa_210	5	7	0.00000000151645
Populus trichocarpa	Chr06	13	CH_ptr_649	3	3	0.000272151
Populus trichocarpa	Chr15	13	CH_ptr_435	6	39	0.00000506899
Populus trichocarpa	Chr18	13	CH_ptr_271	5	7	0.0000000190876
Populus trichocarpa	Chr15	15	CH_ptr_14	6	39	0.00000146706
Setaria italica	scaffold_2	13	CH_sit_287	4	4	0.000000212332
Setaria italica	scaffold_9	13	CH_sit_566	3	3	0.00013949
Solanum lycopersicum	ch01	13	CH_sly_553	3	3	0.000096781
Solanum lycopersicum	ch07	13	CH_sly_270	4	4	0.000000130496
Sorghum bicolor	chr_1	13	CH_sbi_579	3	3	0.000232146
Sorghum bicolor	chr_1	13	CH_sbi_575	4	12	0.000208052
Sorghum bicolor	chr_2	13	CH_sbi_219	5	8	0.0000000427453
Sorghum bicolor	chr_2	13	CH_sbi_282	4	4	0.000000425286
Sorghum bicolor	chr_7	13	CH_sbi_396	4	7	0.0000148194
Vitis vinifera	chr11	13	CH_vvi_253	4	4	0.000000129267
Vitis vinifera	chr12	13	CH_vvi_495	3	3	0.000090453
Vitis vinifera	chr3	13	CH_vvi_153	5	5	0.000000000179882
Zea mays	1	13	CH_zma_364	3	3	0.000123338
Zea mays	7	13	CH_zma_210	4	6	0.00000259945

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