CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g80600

Gene name WIN1 (HOPW1-1-INTERACTING 1)

Module size 9 genes

NF 0.46

%ile 65.1

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
0.40 50.8 1.00 At1g80600 844399 WIN1 (HOPW1-1-INTERACTING 1) Encodes HopW1-1-Interacting protein 1 (WIN1). Interacts with the P. syringae effector HopW1-1. WIN1 is a putative acetylornithine transaminase. Modulates plant defenses against bacteria. Three WIN proteins are identified so far (WIN1: AT1G80600; WIN2: AT4G31750; WIN3: AT5G13320). O.I. H.G. S.X.
0.67 81.6 0.93 At3g20320 821576 TGD2 (TRIGALACTOSYLDIACYLGLYCEROL2) Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast. A phosphatidic acid-binding protein with a predicted mycobacterial cell entry domain. It is tethered to the inner chloroplast envelope membrane facing the outer envelope membrane. Presumed bacterial orthologs of TGD1 and TGD2 in Gram-negative bacteria are typically organized in transcriptional units, suggesting their involvement in a common biological process. O.I. H.G. S.X.
0.59 74.7 0.93 At2g39080 818494 binding / catalytic F:binding, catalytic activity;P:metabolic process;C:chloroplast stroma, chloroplast;BOPA O.I. H.G. S.X.
0.53 68.6 0.93 At5g04710 830349 aspartyl aminopeptidase, putative F:aminopeptidase activity, zinc ion binding;P:proteolysis;C:chloroplast, vacuole;BOFMPA O.I. H.G. S.X.
0.52 67.4 0.93 At1g19800 838568 TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1) Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate. O.I. H.G. S.X.
0.46 59.8 0.93 At3g49560 824118 mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein F:protein transporter activity, P-P-bond-hydrolysis-driven protein transmembrane transporter activity;P:protein transport;C:in 6 components;PMO O.I. H.G. S.X.
0.45 58.3 0.95 At2g19940 816513 N-acetyl-gamma-glutamyl-phosphate reductase/ NAD or NADH binding / binding / catalytic/ oxidoreductase, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / protein dimerization F:in 6 functions;P:amino acid metabolic process, response to cadmium ion;C:nucleolus, chloroplast stroma, chloroplast, membrane;BOAFP O.I. H.G. S.X.
0.44 57.2 0.92 At1g06820 837193 CRTISO (CAROTENOID ISOMERASE) Encodes carotenoid isomerase. Catalyzes the isomerization of poly-cis-carotenoids to all-trans-carotenoids. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene. O.I. H.G. S.X.
0.28 30.3 0.94 At5g19370 832057 rhodanese-like domain-containing protein / PPIC-type PPIASE domain-containing protein F:isomerase activity;P:biological_process unknown;C:chloroplast;BOMFPA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.40	50.8	1.00	At1g80600	844399	WIN1 (HOPW1-1-INTERACTING 1)	Encodes HopW1-1-Interacting protein 1 (WIN1). Interacts with the P. syringae effector HopW1-1. WIN1 is a putative acetylornithine transaminase. Modulates plant defenses against bacteria. Three WIN proteins are identified so far (WIN1: AT1G80600; WIN2: AT4G31750; WIN3: AT5G13320).	O.I.	H.G.	S.X.
0.67	81.6	0.93	At3g20320	821576	TGD2 (TRIGALACTOSYLDIACYLGLYCEROL2)	Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast. A phosphatidic acid-binding protein with a predicted mycobacterial cell entry domain. It is tethered to the inner chloroplast envelope membrane facing the outer envelope membrane. Presumed bacterial orthologs of TGD1 and TGD2 in Gram-negative bacteria are typically organized in transcriptional units, suggesting their involvement in a common biological process.	O.I.	H.G.	S.X.
0.59	74.7	0.93	At2g39080	818494	binding / catalytic	F:binding, catalytic activity;P:metabolic process;C:chloroplast stroma, chloroplast;BOPA	O.I.	H.G.	S.X.
0.53	68.6	0.93	At5g04710	830349	aspartyl aminopeptidase, putative	F:aminopeptidase activity, zinc ion binding;P:proteolysis;C:chloroplast, vacuole;BOFMPA	O.I.	H.G.	S.X.
0.52	67.4	0.93	At1g19800	838568	TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1)	Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate.	O.I.	H.G.	S.X.
0.46	59.8	0.93	At3g49560	824118	mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein	F:protein transporter activity, P-P-bond-hydrolysis-driven protein transmembrane transporter activity;P:protein transport;C:in 6 components;PMO	O.I.	H.G.	S.X.
0.45	58.3	0.95	At2g19940	816513	N-acetyl-gamma-glutamyl-phosphate reductase/ NAD or NADH binding / binding / catalytic/ oxidoreductase, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / protein dimerization	F:in 6 functions;P:amino acid metabolic process, response to cadmium ion;C:nucleolus, chloroplast stroma, chloroplast, membrane;BOAFP	O.I.	H.G.	S.X.
0.44	57.2	0.92	At1g06820	837193	CRTISO (CAROTENOID ISOMERASE)	Encodes carotenoid isomerase. Catalyzes the isomerization of poly-cis-carotenoids to all-trans-carotenoids. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene.	O.I.	H.G.	S.X.
0.28	30.3	0.94	At5g19370	832057	rhodanese-like domain-containing protein / PPIC-type PPIASE domain-containing protein	F:isomerase activity;P:biological_process unknown;C:chloroplast;BOMFPA	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
78.8 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
74.6 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.6 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.7 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
71.4 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.7 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
65.4 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.5 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
57.3 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.1 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
54.9 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.7 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
50.9 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.8 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.5 99.8 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
47.3 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.7 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.1 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.7 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.6 99.1 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
9.4 99.1 GSM247627 Col-0-SH-rep1 GSE9816 Gene expression profiling of sav mutants
9.2 99.1 GSM157377 Truman_1-5_Pst-DC3000(hrpA)-4hpi_Rep2_ATH1 GSE6831 Systemic response to avirulent bacterial infection
9.1 99.1 GSM75510 Col-0 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
8.7 99.0 E-ATMX-33-raw-cel-1562596288

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
78.8	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
74.6	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.6	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.7	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.4	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.7	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
65.4	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.5	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
57.3	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.1	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.9	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.7	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
50.9	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.8	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.5	99.8	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
47.3	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.7	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.1	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.7	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.6	99.1	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
9.4	99.1	GSM247627	Col-0-SH-rep1	GSE9816	Gene expression profiling of sav mutants
9.2	99.1	GSM157377	Truman_1-5_Pst-DC3000(hrpA)-4hpi_Rep2_ATH1	GSE6831	Systemic response to avirulent bacterial infection
9.1	99.1	GSM75510	Col-0 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.7	99.0	E-ATMX-33-raw-cel-1562596288

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.182 1 GO:0009662 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an etioplast. An etioplast is a plastid arrested in the development of chloroplasts from proplastids due to absence of light or low light conditions.
0.091 1 GO:0016117 The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.061 1 GO:0006520 The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents.

SF	Genes	GO ID	Process Name
0.182	1	GO:0009662	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an etioplast. An etioplast is a plastid arrested in the development of chloroplasts from proplastids due to absence of light or low light conditions.
0.091	1	GO:0016117	The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.061	1	GO:0006520	The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.068 2 00330 Arginine and proline metabolism
0.065 1 00906 Carotenoid biosynthesis
0.023 2 01064 Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

SF	Genes	KEGG ID	Pathway name
0.068	2	00330	Arginine and proline metabolism
0.065	1	00906	Carotenoid biosynthesis
0.023	2	01064	Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

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

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Gene ID	At1g80600
Gene name	WIN1 (HOPW1-1-INTERACTING 1)
Module size	9 genes
NF	0.46
%ile	65.1

Co-expression analysis

Gene ID At1g80600 Gene name WIN1 (HOPW1-1-INTERACTING 1) Module size 9 genes NF 0.46 %ile 65.1

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 KEGG0.068200330Arginine and proline metabolism0.065100906Carotenoid biosynthesis0.023201064Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

Inter-species module comparison

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

Gene ID At1g80600

Gene name WIN1 (HOPW1-1-INTERACTING 1)

Module size 9 genes

NF 0.46

%ile 65.1

: 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
0.068 2 00330 Arginine and proline metabolism
0.065 1 00906 Carotenoid biosynthesis
0.023 2 01064 Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

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