CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g01080

Gene name unknown protein

Module size 5 genes

NF 0.02

%ile 1.2

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. O.I. H.G. S.X. Other DB
0.22 17.5 1.00 At4g01080 827902 unknown protein F:unknown;P:biological_process unknown;C:cellular_component unknown;PF O.I. H.G. S.X.
0.36 43.6 0.63 At2g20340 816553 tyrosine decarboxylase, putative F:pyridoxal phosphate binding, carboxy-lyase activity, catalytic activity, tyrosine decarboxylase activity;P:amino acid metabolic process, response to wounding;C:cellular_component unknown;MBOFPAV O.I. H.G. S.X.
0.04 0.9 0.65 At1g32900 840184 starch synthase, putative F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM O.I. H.G. S.X.
0.03 0.6 0.62 At5g24150 832480 SQP1 squalene monooxygenase gene homolog O.I. H.G. S.X.
- 0.0 0.65 At5g52320 835308 CYP96A4 member of CYP96A O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.22	17.5	1.00	At4g01080	827902	unknown protein	F:unknown;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.36	43.6	0.63	At2g20340	816553	tyrosine decarboxylase, putative	F:pyridoxal phosphate binding, carboxy-lyase activity, catalytic activity, tyrosine decarboxylase activity;P:amino acid metabolic process, response to wounding;C:cellular_component unknown;MBOFPAV	O.I.	H.G.	S.X.
0.04	0.9	0.65	At1g32900	840184	starch synthase, putative	F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM	O.I.	H.G.	S.X.
0.03	0.6	0.62	At5g24150	832480	SQP1	squalene monooxygenase gene homolog	O.I.	H.G.	S.X.
-	0.0	0.65	At5g52320	835308	CYP96A4	member of CYP96A	O.I.	H.G.	S.X.

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
376.0 100.0 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
330.1 100.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
60.6 99.8 GSM10456 WT Post-Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
34.9 99.7 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.7 99.6 GSM10454 WT Post-Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
20.8 99.6 GSM10484 lec1-1 Post-Mature Green Seed 2 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
18.5 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.3 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.7 99.5 GSM10483 lec1-1 Post-Mature Green Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
16.6 99.5 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
16.3 99.5 GSM131706 ATGE_84_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.3 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.4 99.4 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.2 99.4 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.7 99.4 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.7 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.0 99.4 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.0 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.9 99.3 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.7 99.3 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.9 99.3 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.7 99.3 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4 99.3 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.2 99.2 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.1 99.2 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2 99.2 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0 99.2 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9 99.1 GSM131707 ATGE_84_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
8.9 99.0 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
376.0	100.0	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
330.1	100.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
60.6	99.8	GSM10456	WT Post-Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
34.9	99.7	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.7	99.6	GSM10454	WT Post-Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
20.8	99.6	GSM10484	lec1-1 Post-Mature Green Seed 2	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
18.5	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.3	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.7	99.5	GSM10483	lec1-1 Post-Mature Green Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
16.6	99.5	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
16.3	99.5	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.3	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.4	99.4	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.2	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.7	99.4	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.7	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.0	99.4	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.0	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.9	99.3	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.7	99.3	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.9	99.3	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.7	99.3	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4	99.3	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.2	99.2	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.1	99.2	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2	99.2	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9	99.1	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
8.9	99.0	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0009250 The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.069 1 GO:0006520 The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents.
0.069 1 GO:0016126 The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.

SF	Genes	GO ID	Process Name
0.286	1	GO:0009250	The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.069	1	GO:0006520	The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents.
0.069	1	GO:0016126	The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.154 1 00901 Indole alkaloid biosynthesis
0.133 1 00950 Isoquinoline alkaloid biosynthesis
0.105 1 00340 Histidine metabolism

SF	Genes	KEGG ID	Pathway name
0.154	1	00901	Indole alkaloid biosynthesis
0.133	1	00950	Isoquinoline alkaloid biosynthesis
0.105	1	00340	Histidine metabolism

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays

Back to the CoP portal site

Back to the KAGIANA project homepage

Gene ID	At4g01080
Gene name	unknown protein
Module size	5 genes
NF	0.02
%ile	1.2

Co-expression analysis

Gene ID At4g01080 Gene name unknown protein Module size 5 genes NF 0.02 %ile 1.2

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.154100901Indole alkaloid biosynthesis0.133100950Isoquinoline alkaloid biosynthesis0.105100340Histidine metabolism

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At4g01080

Gene name unknown protein

Module size 5 genes

NF 0.02

%ile 1.2

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.154 1 00901 Indole alkaloid biosynthesis
0.133 1 00950 Isoquinoline alkaloid biosynthesis
0.105 1 00340 Histidine metabolism

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays