PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: Mapman term
Identifier: 27.3.24
Description: RNA.regulation of transcription.MADS box transcription factor family

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	17	CH_ath_179	8	57	0.000000338346
Arabidopsis thaliana	5	17	CH_ath_217	4	4	0.00000302415
Arabidopsis thaliana	5	18	CH_ath_49	12	164	0.00000000535994
Capsella rubella	scaffold_2	17	CH_cru_28	9	10	5.08516e-16
Capsella rubella	scaffold_4	17	CH_cru_211	4	4	0.0000176527
Capsella rubella	scaffold_6	17	CH_cru_86	6	7	0.00000000305247
Capsella rubella	scaffold_2	18	CH_cru_31	13	154	0.0000000367508
Citrus sinensis	scaffold00236	17	CH_csi_212	3	3	0.000376832
Eucalyptus grandis	scaffold_11	17	CH_egr_30	15	18	1.28156e-31
Eucalyptus grandis	scaffold_2	17	CH_egr_855	3	3	0.000885256
Eucalyptus grandis	scaffold_4	17	CH_egr_856	3	3	0.000885256
Eucalyptus grandis	scaffold_5	17	CH_egr_549	4	4	0.00000256919
Eucalyptus grandis	scaffold_5	17	CH_egr_407	8	45	0.0000000323563
Eucalyptus grandis	scaffold_6	17	CH_egr_712	5	19	0.0000829914
Eucalyptus grandis	scaffold_9	17	CH_egr_497	5	8	0.000000410381
Eucalyptus grandis	scaffold_11	18	CH_egr_33	15	18	1.28156e-31
Glycine max	Gm10	17	CH_gma_42	9	12	5.19722e-16
Glycine max	Gm10	17	CH_gma_266	4	4	0.00000661957
Glycine max	Gm11	17	CH_gma_105	6	8	0.00000000197461
Glycine max	Gm18	17	CH_gma_221	5	8	0.0000012068
Glycine max	Gm20	17	CH_gma_139	5	5	0.000000021728
Glycine max	Gm10	18	CH_gma_31	10	28	0.0000000000000946732
Gossypium raimondii	Chr10	17	CH_gra_47	9	12	4.32576e-16
Gossypium raimondii	Chr12	17	CH_gra_149	5	7	0.000000356144
Gossypium raimondii	Chr13	17	CH_gra_138	5	6	0.000000102041
Malus domestica	1	17	CH_mdo_96	4	4	0.000000542202
Malus domestica	12	17	CH_mdo_257	3	3	0.00029365
Manihot esculenta	scaffold04043	17	CH_mes_265	3	3	0.000962181
Manihot esculenta	scaffold08359	17	CH_mes_266	3	3	0.000962181
Manihot esculenta	scaffold08860	17	CH_mes_264	3	3	0.000962181
Manihot esculenta	scaffold12086	17	CH_mes_111	4	4	0.00000335495
Populus trichocarpa	Chr03	17	CH_ptr_204	5	7	0.0000000991992
Populus trichocarpa	Chr07	17	CH_ptr_311	5	15	0.0000139458
Prunus persica	scaffold_1	17	CH_ppe_121	8	29	0.00000000041871
Prunus persica	scaffold_7	17	CH_ppe_430	3	3	0.000665041
Prunus persica	scaffold_1	18	CH_ppe_75	12	233	0.00000010813
Ricinus communis	29693	17	CH_rco_287	3	4	0.000999039
Solanum lycopersicum	ch01	17	CH_sly_225	4	4	0.00000234001
Solanum lycopersicum	ch01	17	CH_sly_472	3	3	0.000829153
Vitis vinifera	chr3	17	CH_vvi_161	5	8	0.00000004868

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