PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis lyrata	scaffold_1	1	CH_aly_91	6	6	0.000000487096
Arabidopsis lyrata	scaffold_3	1	CH_aly_92	6	6	0.000000487096
Arabidopsis lyrata	scaffold_3	2	CH_aly_130	7	7	0.000000701768
Arabidopsis lyrata	scaffold_3	3	CH_aly_176	7	7	0.00000281554
Arabidopsis thaliana	2	1	CH_ath_255	6	7	0.000115418
Arabidopsis thaliana	2	2	CH_ath_306	8	15	0.000140685
Capsella rubella	scaffold_2	2	CH_cru_350	5	5	0.000930262
Glycine max	Gm11	2	CH_gma_472	6	8	0.000916252
Glycine max	Gm18	2	CH_gma_471	6	8	0.000916252
Medicago truncatula	chr3	2	CH_mtr_394	7	12	0.00000978181
Medicago truncatula	chr3	3	CH_mtr_586	7	12	0.0000589967
Medicago truncatula	chr2	6	CH_mtr_156	10	26	0.00000252618
Oryza sativa ssp. japonica	5	3	CH_osa_447	9	34	0.00051277
Solanum lycopersicum	ch06	6	CH_sly_149	33	283	0.000235106
Solanum tuberosum	chr06	1	CH_stu_425	5	6	0.00020846
Solanum tuberosum	chr06	5	CH_stu_174	29	296	0.000420189
Zea mays	2	1	CH_zma_229	6	12	0.000837436

GO term	Description	Number of clusters
GO:0000228	nuclear chromosome	2
GO:0000311	plastid large ribosomal subunit	4
GO:0000315	organellar large ribosomal subunit	1
GO:0000775	chromosome, centromeric region	2
GO:0000776	kinetochore	1
GO:0000779	condensed chromosome, centromeric region	1
GO:0000784	nuclear chromosome, telomeric region	4
GO:0000785	chromatin	6
GO:0000786	nucleosome	102
GO:0000795	synaptonemal complex	4
GO:0000796	condensin complex	20
GO:0000811	GINS complex	1
GO:0000922	spindle pole	6
GO:0000930	gamma-tubulin complex	2
GO:0005657	replication fork	2
GO:0005662	DNA replication factor A complex	2
GO:0005664	nuclear origin of replication recognition complex	11
GO:0005694	chromosome	6
GO:0005720	nuclear heterochromatin	2
GO:0005815	microtubule organizing center	3
GO:0005819	spindle	3
GO:0005840	ribosome	21
GO:0005856	cytoskeleton	5
GO:0005871	kinesin complex	19
GO:0005874	microtubule	2
GO:0005884	actin filament	5
GO:0008290	F-actin capping protein complex	4
GO:0010370	perinucleolar chromocenter	4
GO:0015629	actin cytoskeleton	7
GO:0015934	large ribosomal subunit	5
GO:0015935	small ribosomal subunit	6
GO:0016459	myosin complex	16
GO:0022626	cytosolic ribosome	2
GO:0022627	cytosolic small ribosomal subunit	11
GO:0030896	checkpoint clamp complex	3
GO:0030915	Smc5-Smc6 complex	7
GO:0030981	cortical microtubule cytoskeleton	8
GO:0031011	Ino80 complex	11
GO:0033557	Slx1-Slx4 complex	1
GO:0043596	nuclear replication fork	4
GO:0043601	nuclear replisome	1
GO:0044391	ribosomal subunit	13
GO:0044427	chromosomal part	23
GO:0070652	HAUS complex	13

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