PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Beta vulgaris	Bvchr9.sca026	1	CH_bvu_214	5	6	0.000610817
Brassica rapa	A10	1	CH_bra_152	5	6	0.000217501
Carica papaya	supercontig_84	1	CH_cpa_153	9	41	0.000317185
Chlamydomonas reinhardtii	chromosome_13	6	CH_cre_25	10	27	0.000107056
Glycine max	Gm02	4	CH_gma_78	20	263	0.000718264
Gossypium raimondii	Chr03	1	CH_gra_99	7	7	0.0000000111675
Gossypium raimondii	Chr03	2	CH_gra_115	7	7	0.0000000368283
Gossypium raimondii	Chr03	3	CH_gra_145	7	7	0.0000000782791
Malus domestica	2	1	CH_mdo_239	7	30	0.000730068
Medicago truncatula	chr4	2	CH_mtr_597	10	78	0.00028307
Medicago truncatula	chr4	5	CH_mtr_202	10	78	0.00028307
Medicago truncatula	chr1	6	CH_mtr_211	17	211	0.000117447
Medicago truncatula	chr3	6	CH_mtr_181	10	46	0.0000120751
Oryza sativa ssp. japonica	5	1	CH_osa_383	20	76	0.000833168
Oryza sativa ssp. japonica	5	10	CH_osa_11	57	298	0.000000000468081
Oryza sativa ssp. japonica	5	11	CH_osa_27	52	304	0.00000156247
Oryza sativa ssp. japonica	5	12	CH_osa_28	53	304	0.00000098925
Solanum lycopersicum	ch10	1	CH_sly_207	8	12	0.00000206175
Solanum lycopersicum	ch10	2	CH_sly_230	8	12	0.00000364985
Solanum lycopersicum	ch10	3	CH_sly_212	9	12	0.000000137113
Solanum lycopersicum	ch10	5	CH_sly_99	10	31	0.000148974
Solanum lycopersicum	ch10	6	CH_sly_118	10	23	0.0000161445

GO term	Description	Number of clusters
GO:0000049	tRNA binding	2
GO:0000499	base pairing with mRNA	57
GO:0003725	double-stranded RNA binding	5
GO:0003729	mRNA binding	1
GO:0003730	mRNA 3'-UTR binding	12
GO:0003746	translation elongation factor activity	47
GO:0003747	translation release factor activity	1
GO:0008097	5S rRNA binding	7
GO:0008143	poly(A) RNA binding	4
GO:0008312	7S RNA binding	1
GO:0016149	translation release factor activity, codon specific	7
GO:0017069	snRNA binding	9
GO:0017070	U6 snRNA binding	3
GO:0019843	rRNA binding	12
GO:0030619	U1 snRNA binding	4
GO:0035197	siRNA binding	3
GO:0035198	miRNA binding	4
GO:0097157	pre-mRNA intronic binding	6

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