PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Information

Type: Mapman term
Identifier: 27.2
Description: RNA.transcription

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	2	17	CH_ath_390	3	3	0.000859298
Arabidopsis thaliana	chloroplast	17	CH_ath_391	3	3	0.000859298
Arabidopsis thaliana	chloroplast	19	CH_ath_104	3	3	0.00071233
Oryza sativa ssp. japonica	10	17	CH_osa_425	15	80	0.000844309
Oryza sativa ssp. japonica	10	17	CH_osa_250	13	42	0.0000101318
Oryza sativa ssp. japonica	12	17	CH_osa_340	12	42	0.000143394
Oryza sativa ssp. japonica	3	17	CH_osa_388	9	22	0.000389386
Oryza sativa ssp. japonica	5	17	CH_osa_371	15	73	0.000225455
Oryza sativa ssp. japonica	5	17	CH_osa_317	16	79	0.0000861146
Oryza sativa ssp. japonica	6	17	CH_osa_274	16	73	0.0000249533
Oryza sativa ssp. japonica	8	17	CH_osa_231	15	57	0.00000537507
Oryza sativa ssp. japonica	10	18	CH_osa_83	32	278	0.00000669599
Oryza sativa ssp. japonica	10	18	CH_osa_86	13	42	0.0000101318
Oryza sativa ssp. japonica	12	18	CH_osa_90	18	91	0.000012487
Oryza sativa ssp. japonica	4	18	CH_osa_99	31	282	0.0000407213
Oryza sativa ssp. japonica	4	18	CH_osa_73	34	299	0.00000249163
Oryza sativa ssp. japonica	5	18	CH_osa_40	42	299	0.0000000000080125
Oryza sativa ssp. japonica	5	18	CH_osa_48	38	292	0.00000000267523
Oryza sativa ssp. japonica	6	18	CH_osa_96	19	106	0.0000234863
Oryza sativa ssp. japonica	7	18	CH_osa_113	22	162	0.000242251
Oryza sativa ssp. japonica	8	18	CH_osa_78	15	57	0.00000537507
Oryza sativa ssp. japonica	8	18	CH_osa_61	35	293	0.000000320206
Oryza sativa ssp. japonica	10	19	CH_osa_14	13	42	0.00000948858
Oryza sativa ssp. japonica	10	19	CH_osa_44	15	80	0.000786578
Oryza sativa ssp. japonica	3	19	CH_osa_36	9	22	0.000371695
Oryza sativa ssp. japonica	5	19	CH_osa_24	16	79	0.0000797723
Oryza sativa ssp. japonica	5	19	CH_osa_29	15	73	0.000209814
Oryza sativa ssp. japonica	6	19	CH_osa_18	16	73	0.0000230942
Oryza sativa ssp. japonica	8	19	CH_osa_12	15	57	0.00000498988
Oryza sativa ssp. japonica	10	20	CH_osa_24	13	42	0.00000948858
Oryza sativa ssp. japonica	10	20	CH_osa_22	32	278	0.00000585614
Oryza sativa ssp. japonica	12	20	CH_osa_43	16	91	0.000687077
Oryza sativa ssp. japonica	4	20	CH_osa_17	34	299	0.00000216216
Oryza sativa ssp. japonica	4	20	CH_osa_31	31	282	0.0000358352
Oryza sativa ssp. japonica	5	20	CH_osa_4	42	299	0.00000000000661039
Oryza sativa ssp. japonica	5	20	CH_osa_8	37	292	0.0000000112183
Oryza sativa ssp. japonica	6	20	CH_osa_26	19	106	0.0000214881
Oryza sativa ssp. japonica	7	20	CH_osa_37	22	162	0.000219902
Oryza sativa ssp. japonica	8	20	CH_osa_21	15	57	0.00000498988
Oryza sativa ssp. japonica	8	20	CH_osa_11	35	293	0.000000276054
Physcomitrella patens	scaffold_29	17	CH_ppa_12	4	4	0.00000702187
Populus trichocarpa	Chr17	17	CH_ptr_143	8	27	0.00000000241898
Populus trichocarpa	Chr19	17	CH_ptr_295	4	4	0.00000718893
Populus trichocarpa	Chr17	18	CH_ptr_117	10	240	0.000981237
Setaria italica	scaffold_1	17	CH_sit_435	4	9	0.000720123
Solanum lycopersicum	ch01	17	CH_sly_51	10	17	0.0000000000000296022
Solanum lycopersicum	ch08	17	CH_sly_111	6	6	0.0000000014483
Solanum lycopersicum	ch12	17	CH_sly_150	8	24	0.0000000327167
Solanum lycopersicum	ch01	18	CH_sly_42	10	17	0.0000000000000296022
Zea mays	10	17	CH_zma_17	8	14	0.00000000000432352
Zea mays	5	17	CH_zma_122	5	12	0.0000209366
Zea mays	10	18	CH_zma_34	10	227	0.00079499
Zea mays	chloroplast	19	CH_zma_21	3	3	0.000922773

Functional clusters experiments

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