PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0009507
Description: chloroplast

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	chloroplast	1	CH_atr_3	24	66	4.57407e-46
Arabidopsis lyrata	scaffold_5	1	CH_aly_141	5	43	0.0000159288
Arabidopsis lyrata	scaffold_3	2	CH_aly_306	12	22	0.000547815
Arabidopsis lyrata	scaffold_1	3	CH_aly_192	9	9	0.00000431374
Arabidopsis lyrata	scaffold_2	3	CH_aly_139	10	10	0.000000345028
Arabidopsis lyrata	scaffold_3	3	CH_aly_381	12	22	0.00066358
Arabidopsis lyrata	scaffold_8	3	CH_aly_185	10	11	0.00000351933
Arabidopsis lyrata	scaffold_3	5	CH_aly_78	12	22	0.000547815
Arabidopsis lyrata	scaffold_3	6	CH_aly_96	12	22	0.00066358
Arabidopsis lyrata	scaffold_8	6	CH_aly_46	10	11	0.00000351933
Capsella rubella	scaffold_5	1	CH_cru_139	3	3	0.0000200984
Capsella rubella	scaffold_2	3	CH_cru_72	27	52	0.000000000121136
Capsella rubella	scaffold_2	6	CH_cru_30	27	52	0.000000000121136
Chlamydomonas reinhardtii	chloroplast	1	CH_cre_2	26	79	3.14796e-41
Chlamydomonas reinhardtii	chloroplast	7	CH_cre_2	22	79	1.62753e-34
Citrus sinensis	chloroplast	1	CH_csi_3	24	73	1.92834e-42
Eucalyptus grandis	scaffold_3	3	CH_egr_731	8	10	0.000138311
Glycine max	chloroplast	1	CH_gma_3	24	73	2.88549e-43
Gossypium raimondii	Chr04	1	CH_gra_116	4	4	0.000000180755
Oryza sativa ssp. japonica	4	1	CH_osa_3	24	49	1.48167e-37
Oryza sativa ssp. japonica	7	1	CH_osa_175	5	6	0.0000011787
Oryza sativa ssp. japonica	8	1	CH_osa_33	11	18	9.76261e-17
Oryza sativa ssp. japonica	chloroplast	1	CH_osa_4	26	80	3.52164e-35
Oryza sativa ssp. japonica	4	2	CH_osa_6	28	41	5.34082e-27
Oryza sativa ssp. japonica	4	3	CH_osa_7	29	41	1.04772e-28
Oryza sativa ssp. japonica	4	4	CH_osa_4	24	49	1.48167e-37
Oryza sativa ssp. japonica	8	4	CH_osa_30	11	18	9.76261e-17
Oryza sativa ssp. japonica	chloroplast	4	CH_osa_2	40	160	5.32284e-51
Oryza sativa ssp. japonica	4	5	CH_osa_6	31	53	4.02348e-27
Oryza sativa ssp. japonica	4	6	CH_osa_6	33	53	2.76643e-30
Oryza sativa ssp. japonica	4	7	CH_osa_4	12	43	0.00000000000000531173
Oryza sativa ssp. japonica	7	7	CH_osa_18	5	6	0.00000069652
Oryza sativa ssp. japonica	8	7	CH_osa_7	9	18	0.00000000000120215
Oryza sativa ssp. japonica	10	8	CH_osa_12	9	12	0.000000108094
Oryza sativa ssp. japonica	10	9	CH_osa_12	9	12	0.000000115038
Oryza sativa ssp. japonica	4	9	CH_osa_4	18	43	0.00000000000046023
Oryza sativa ssp. japonica	4	10	CH_osa_6	12	43	0.00000000000000531173
Oryza sativa ssp. japonica	4	12	CH_osa_6	18	43	0.00000000000046023
Populus trichocarpa	chloroplast	1	CH_ptr_5	24	81	1.97478e-42
Populus trichocarpa	chloroplast	7	CH_ptr_2	18	92	1.21186e-29
Solanum lycopersicum	ch02	1	CH_sly_258	4	4	0.0000310916
Solanum lycopersicum	ch02	1	CH_sly_125	6	7	0.00000000626894
Solanum lycopersicum	ch09	1	CH_sly_161	5	5	0.000000167696
Solanum lycopersicum	ch12	1	CH_sly_93	9	25	0.000000000254703
Solanum lycopersicum	ch01	3	CH_sly_494	8	10	0.000188526
Solanum lycopersicum	ch02	4	CH_sly_66	11	119	0.00000231655
Solanum tuberosum	chloroplast	1	CH_stu_6	24	65	1.13977e-40
Solanum tuberosum	chr01	1	CH_stu_510	3	3	0.000859834
Solanum tuberosum	chr05	1	CH_stu_511	3	3	0.000859834
Solanum tuberosum	chr05	7	CH_stu_9	3	3	0.000309287
Theobroma cacao	scaffold_8	2	CH_tca_273	8	10	0.000170714
Theobroma cacao	scaffold_8	3	CH_tca_333	8	10	0.00017386
Vitis vinifera	chloroplast	1	CH_vvi_6	24	78	6.9358e-41
Zea mays	10	1	CH_zma_164	4	6	0.000118425
Zea mays	chloroplast	1	CH_zma_1	29	45	2.39522e-55
Zea mays	chloroplast	1	CH_zma_6	22	80	1.01158e-30
Zea mays	chloroplast	3	CH_zma_9	30	58	2.82229e-19
Zea mays	10	7	CH_zma_6	4	6	0.0000268336

Available child term results

GO term	Description	Number of clusters
GO:0009535	chloroplast thylakoid membrane	54
GO:0009543	chloroplast thylakoid lumen	1
GO:0009569	chloroplast starch grain	2
GO:0009573	chloroplast ribulose bisphosphate carboxylase complex	4
GO:0009706	chloroplast inner membrane	2
GO:0009707	chloroplast outer membrane	1
GO:0009941	chloroplast envelope	8
GO:0010287	plastoglobule	7
GO:0030095	chloroplast photosystem II	1
GO:0031357	integral to chloroplast inner membrane	4
GO:0031897	Tic complex	2
GO:0031969	chloroplast membrane	4
GO:0044434	chloroplast part	41

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