PLAZA 3.0 Dicots : Functional Clustering

Functional clusters

Information

Type: GO term
Identifier: GO:0055114
Description: oxidation-reduction process

Cluster overview

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Amborella trichopoda	scaffold00071	1	CH_atr_114	8	10	0.00000701985
Amborella trichopoda	scaffold00071	2	CH_atr_124	8	10	0.0000113203
Amborella trichopoda	scaffold00071	3	CH_atr_137	9	10	0.00000032876
Amborella trichopoda	scaffold00022	4	CH_atr_40	15	54	0.0000522885
Amborella trichopoda	scaffold00022	5	CH_atr_47	15	54	0.000117951
Amborella trichopoda	scaffold00071	6	CH_atr_71	10	19	0.000101801
Arabidopsis lyrata	scaffold_2	2	CH_aly_80	23	80	0.0000000120761
Arabidopsis lyrata	scaffold_2	3	CH_aly_66	25	79	0.000000000433572
Arabidopsis thaliana	1	4	CH_ath_108	39	268	0.000311226
Arabidopsis thaliana	1	5	CH_ath_108	40	268	0.000122169
Arabidopsis thaliana	1	6	CH_ath_72	43	268	0.00000832492
Beta vulgaris	Bvchr5.sca002	2	CH_bvu_224	13	35	0.000268946
Beta vulgaris	Bvchr5.sca002	3	CH_bvu_318	13	35	0.000504502
Brassica rapa	A05	3	CH_bra_189	7	7	0.0000329217
Brassica rapa	A09	3	CH_bra_159	8	9	0.0000142169
Capsella rubella	scaffold_6	1	CH_cru_115	9	11	0.0000040024
Capsella rubella	scaffold_8	1	CH_cru_220	9	16	0.000654112
Chlamydomonas reinhardtii	chromosome_9	6	CH_cre_26	10	21	0.000152611
Eucalyptus grandis	scaffold_1	1	CH_egr_586	7	8	0.00041848
Eucalyptus grandis	scaffold_2	1	CH_egr_311	9	9	0.000000168089
Eucalyptus grandis	scaffold_4	1	CH_egr_264	13	18	0.0000000102911
Eucalyptus grandis	scaffold_5	1	CH_egr_164	18	28	0.000000000006091
Eucalyptus grandis	scaffold_1	2	CH_egr_759	7	8	0.000583565
Eucalyptus grandis	scaffold_2	2	CH_egr_413	9	9	0.000000258648
Eucalyptus grandis	scaffold_5	2	CH_egr_219	18	28	0.0000000000140637
Eucalyptus grandis	scaffold_8	2	CH_egr_686	8	10	0.000180511
Eucalyptus grandis	scaffold_2	3	CH_egr_505	9	9	0.000000508181
Eucalyptus grandis	scaffold_4	3	CH_egr_367	17	29	0.00000000293196
Eucalyptus grandis	scaffold_5	3	CH_egr_279	18	28	0.000000000052032
Eucalyptus grandis	scaffold_8	3	CH_egr_249	13	13	0.00000000000773476
Eucalyptus grandis	scaffold_10	4	CH_egr_196	10	14	0.00000756602
Eucalyptus grandis	scaffold_11	4	CH_egr_184	10	13	0.00000227591
Eucalyptus grandis	scaffold_4	4	CH_egr_169	14	26	0.000000441625
Eucalyptus grandis	scaffold_4	4	CH_egr_171	11	15	0.000000568845
Eucalyptus grandis	scaffold_4	4	CH_egr_140	13	18	0.0000000102911
Eucalyptus grandis	scaffold_5	4	CH_egr_115	18	28	0.000000000006091
Eucalyptus grandis	scaffold_11	5	CH_egr_211	10	13	0.00000364572
Eucalyptus grandis	scaffold_4	5	CH_egr_202	11	15	0.000000953487
Eucalyptus grandis	scaffold_4	5	CH_egr_200	14	26	0.00000083688
Eucalyptus grandis	scaffold_5	5	CH_egr_121	18	28	0.0000000000140637
Eucalyptus grandis	scaffold_11	6	CH_egr_247	10	13	0.00000762242
Eucalyptus grandis	scaffold_4	6	CH_egr_182	17	29	0.00000000293196
Eucalyptus grandis	scaffold_5	6	CH_egr_152	18	28	0.000000000052032
Eucalyptus grandis	scaffold_8	6	CH_egr_144	13	13	0.00000000000773476
Fragaria vesca	LG2	4	CH_fve_36	12	25	0.00000174025
Fragaria vesca	LG2	4	CH_fve_60	31	242	0.000427943
Fragaria vesca	LG5	4	CH_fve_30	10	14	0.00000029716
Fragaria vesca	LG2	5	CH_fve_36	12	25	0.00000300828
Fragaria vesca	LG5	5	CH_fve_31	10	14	0.000000474785
Glycine max	Gm09	1	CH_gma_111	21	61	0.0000000504322
Glycine max	Gm02	3	CH_gma_501	18	63	0.000441216
Glycine max	Gm07	4	CH_gma_75	20	87	0.000529896
Glycine max	Gm09	4	CH_gma_39	21	61	0.0000000504322
Glycine max	Gm02	6	CH_gma_109	18	63	0.000441216
Gossypium raimondii	Chr03	1	CH_gra_58	16	21	0.00000000000791715
Gossypium raimondii	Chr07	1	CH_gra_128	11	15	0.000000920531
Gossypium raimondii	Chr03	2	CH_gra_62	16	21	0.0000000000173575
Gossypium raimondii	Chr07	2	CH_gra_151	11	15	0.00000157607
Gossypium raimondii	Chr03	3	CH_gra_93	16	21	0.0000000000386226
Gossypium raimondii	Chr03	4	CH_gra_38	16	21	0.00000000000791715
Gossypium raimondii	Chr06	4	CH_gra_59	10	13	0.00000355771
Gossypium raimondii	Chr07	4	CH_gra_53	11	15	0.000000920531
Gossypium raimondii	Chr03	5	CH_gra_37	16	21	0.0000000000173575
Gossypium raimondii	Chr07	5	CH_gra_59	11	15	0.00000157607
Gossypium raimondii	Chr03	6	CH_gra_50	16	21	0.0000000000386226
Lotus japonicus	chr4	1	CH_lja_108	12	58	0.000621244
Lotus japonicus	chr4	4	CH_lja_15	18	138	0.00046182
Lotus japonicus	chr4	5	CH_lja_12	19	124	0.0000354291
Malus domestica	5	1	CH_mdo_25	16	39	0.00000000219904
Malus domestica	5	2	CH_mdo_30	16	39	0.00000000452873
Malus domestica	5	4	CH_mdo_6	16	39	0.00000000219904
Malus domestica	5	5	CH_mdo_8	16	39	0.00000000452873
Medicago truncatula	chr8	1	CH_mtr_292	14	48	0.00000170141
Medicago truncatula	chr3	2	CH_mtr_583	13	55	0.000272999
Medicago truncatula	chr8	2	CH_mtr_365	14	48	0.00000319843
Medicago truncatula	chr7	3	CH_mtr_270	13	24	0.0000000100948
Medicago truncatula	chr8	3	CH_mtr_360	16	50	0.000000372098
Medicago truncatula	chr8	4	CH_mtr_134	18	91	0.00000326818
Medicago truncatula	chr3	5	CH_mtr_200	13	55	0.000272999
Medicago truncatula	chr7	6	CH_mtr_115	13	24	0.0000000100948
Oryza sativa ssp. japonica	6	4	CH_osa_75	11	23	0.000000447275
Oryza sativa ssp. japonica	6	5	CH_osa_89	11	23	0.000000727769
Oryza sativa ssp. japonica	6	6	CH_osa_110	11	23	0.00000179688
Oryza sativa ssp. japonica	10	10	CH_osa_27	25	307	0.00000641558
Populus trichocarpa	Chr05	1	CH_ptr_235	8	9	0.0000174949
Populus trichocarpa	Chr05	2	CH_ptr_268	8	9	0.0000253444
Populus trichocarpa	Chr05	3	CH_ptr_359	8	9	0.0000444191
Prunus persica	scaffold_2	1	CH_ppe_149	13	23	0.000000310034
Prunus persica	scaffold_2	2	CH_ppe_186	13	23	0.000000616192
Prunus persica	scaffold_2	3	CH_ppe_236	13	23	0.00000108122
Prunus persica	scaffold_8	4	CH_ppe_66	13	22	0.000000141458
Prunus persica	scaffold_8	5	CH_ppe_73	13	22	0.000000281936
Prunus persica	scaffold_8	6	CH_ppe_92	13	22	0.000000495906
Ricinus communis	29929	1	CH_rco_178	6	6	0.000397001
Ricinus communis	29678	2	CH_rco_244	7	9	0.000932997
Solanum lycopersicum	ch09	1	CH_sly_153	9	9	0.0000000870333
Solanum lycopersicum	ch09	2	CH_sly_165	9	9	0.000000132741
Solanum lycopersicum	ch01	3	CH_sly_512	14	36	0.000259024
Solanum lycopersicum	ch05	3	CH_sly_617	7	8	0.000698002
Solanum lycopersicum	ch09	3	CH_sly_229	9	9	0.000000324504
Solanum tuberosum	chr04	3	CH_stu_782	9	13	0.000985558
Solanum tuberosum	chr02	4	CH_stu_109	10	12	0.00000142759
Solanum tuberosum	chr05	4	CH_stu_117	10	13	0.00000584529
Solanum tuberosum	chr02	5	CH_stu_113	10	12	0.00000216568
Solanum tuberosum	chr05	5	CH_stu_123	10	13	0.00000884511
Solanum tuberosum	chr05	6	CH_stu_143	11	13	0.00000063065
Thellungiella parvula	ch3-4	1	CH_tpa_83	11	25	0.0000466729
Thellungiella parvula	ch3-4	4	CH_tpa_13	11	25	0.0000466729
Thellungiella parvula	ch7-4	4	CH_tpa_9	10	17	0.00000641154
Thellungiella parvula	ch7-4	5	CH_tpa_21	10	17	0.0000138162
Theobroma cacao	scaffold_3	1	CH_tca_209	8	10	0.0000428881
Theobroma cacao	scaffold_5	1	CH_tca_276	6	6	0.000428647
Theobroma cacao	scaffold_7	1	CH_tca_64	12	14	0.000000000507207
Theobroma cacao	scaffold_3	2	CH_tca_235	8	10	0.0000635759
Theobroma cacao	scaffold_5	2	CH_tca_341	6	6	0.000577775
Theobroma cacao	scaffold_3	3	CH_tca_320	8	10	0.000105053
Theobroma cacao	scaffold_5	3	CH_tca_448	6	6	0.000845887
Theobroma cacao	scaffold_5	3	CH_tca_282	7	7	0.0000467454
Theobroma cacao	scaffold_7	4	CH_tca_31	12	14	0.000000000507207
Theobroma cacao	scaffold_7	5	CH_tca_33	12	14	0.000000000918134
Theobroma cacao	scaffold_7	6	CH_tca_50	12	14	0.00000000195782
Vitis vinifera	chr1	1	CH_vvi_170	8	8	0.00000200639
Vitis vinifera	chr5	1	CH_vvi_71	13	14	0.000000000012316
Vitis vinifera	chr1	2	CH_vvi_195	8	8	0.00000305673
Vitis vinifera	chr5	2	CH_vvi_74	13	14	0.0000000000243693
Vitis vinifera	chr1	3	CH_vvi_269	8	8	0.00000709911
Vitis vinifera	chr14	3	CH_vvi_401	9	13	0.000254517
Vitis vinifera	chr5	3	CH_vvi_110	13	14	0.0000000000954379
Vitis vinifera	chr5	4	CH_vvi_44	13	14	0.000000000012316
Vitis vinifera	chr5	5	CH_vvi_43	13	14	0.0000000000243693
Vitis vinifera	chr14	6	CH_vvi_129	10	17	0.000366528
Vitis vinifera	chr5	6	CH_vvi_64	13	14	0.0000000000954379
Zea mays	1	4	CH_zma_33	10	22	0.000161056
Zea mays	10	4	CH_zma_27	38	298	0.0000120525
Zea mays	1	5	CH_zma_37	10	22	0.000247924
Zea mays	10	5	CH_zma_28	38	298	0.0000421443
Zea mays	1	6	CH_zma_52	10	22	0.00055486

Available child term results

GO term	Description	Number of clusters
GO:0001561	fatty acid alpha-oxidation	13
GO:0006069	ethanol oxidation	3
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	1
GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	2
GO:0006635	fatty acid beta-oxidation	3
GO:0006788	heme oxidation	1
GO:0009051	pentose-phosphate shunt, oxidative branch	2
GO:0009052	pentose-phosphate shunt, non-oxidative branch	3
GO:0009060	aerobic respiration	3
GO:0009061	anaerobic respiration	3
GO:0009772	photosynthetic electron transport in photosystem II	1
GO:0010205	photoinhibition	2
GO:0010241	ent-kaurene oxidation to kaurenoic acid	3
GO:0010430	fatty acid omega-oxidation	4
GO:0010478	chlororespiration	4
GO:0022900	electron transport chain	38
GO:0022904	respiratory electron transport chain	18
GO:0042773	ATP synthesis coupled electron transport	5
GO:0045333	cellular respiration	5

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