CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g59320

Gene name LTP3 (LIPID TRANSFER PROTEIN 3)

Module size 5 genes

NF 0.46

%ile 64.3

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
0.46 59.8 1.00 At5g59320 836051 LTP3 (LIPID TRANSFER PROTEIN 3) Predicted to encode a PR (pathogenesis-related) protein. Belongs to the lipid transfer protein (PR-14) family with the following members: At2g38540/LTP1, At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5, At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9, At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13, At5g62065/LTP14, At4g08530/LTP15. O.I. H.G. S.X.
0.75 86.9 0.83 At5g59310 836050 LTP4 (LIPID TRANSFER PROTEIN 4) Encodes a member of the lipid transfer protein family. Proteins of this family are generally small (~9 kD), basic, expressed abundantly and contain eight Cys residues. The proteins can bind fatty acids and acylCoA esters and can transfer several different phospholipids. They are localized to the cell wall. The mRNA is present in flowers and siliques, and is strongly up-regulated by abscisic acid. Predicted to be a member of PR-14 pathogenesis-related protein family with the following members: At2g38540/LTP1, At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5, At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9, At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13, At5g62065/LTP14, At4g08530/LTP15. O.I. H.G. S.X.
0.40 50.8 0.57 At1g57750 842150 CYP96A15 (CYTOCHROME P450 96 A1) Encodes a CYP96A15, midchain alkane hydroxylase, involved in cuticular wax biosynthesis. O.I. H.G. S.X.
0.40 50.8 0.53 At4g21650 828252 subtilase family protein F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:plant-type cell wall;BPOFAM O.I. H.G. S.X.
0.25 22.6 0.58 At5g25390 832611 SHN2 (shine2) encodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 12 members in this subfamily including RAP2.11. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.46	59.8	1.00	At5g59320	836051	LTP3 (LIPID TRANSFER PROTEIN 3)	Predicted to encode a PR (pathogenesis-related) protein. Belongs to the lipid transfer protein (PR-14) family with the following members: At2g38540/LTP1, At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5, At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9, At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13, At5g62065/LTP14, At4g08530/LTP15.	O.I.	H.G.	S.X.
0.75	86.9	0.83	At5g59310	836050	LTP4 (LIPID TRANSFER PROTEIN 4)	Encodes a member of the lipid transfer protein family. Proteins of this family are generally small (~9 kD), basic, expressed abundantly and contain eight Cys residues. The proteins can bind fatty acids and acylCoA esters and can transfer several different phospholipids. They are localized to the cell wall. The mRNA is present in flowers and siliques, and is strongly up-regulated by abscisic acid. Predicted to be a member of PR-14 pathogenesis-related protein family with the following members: At2g38540/LTP1, At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5, At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9, At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13, At5g62065/LTP14, At4g08530/LTP15.	O.I.	H.G.	S.X.
0.40	50.8	0.57	At1g57750	842150	CYP96A15 (CYTOCHROME P450 96 A1)	Encodes a CYP96A15, midchain alkane hydroxylase, involved in cuticular wax biosynthesis.	O.I.	H.G.	S.X.
0.40	50.8	0.53	At4g21650	828252	subtilase family protein	F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:plant-type cell wall;BPOFAM	O.I.	H.G.	S.X.
0.25	22.6	0.58	At5g25390	832611	SHN2 (shine2)	encodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 12 members in this subfamily including RAP2.11.	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
140.4 99.9 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
108.8 99.9 GSM311274 Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
104.9 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
104.7 99.9 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
101.9 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
92.2 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
89.5 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
72.8 99.9 GSM311273 Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
68.6 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.7 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.6 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.7 99.7 GSM284385 Arabidopsis GEP6 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
23.5 99.6 GSM75509 Col-0 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
18.0 99.5 GSM284384 Arabidopsis GEP5 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.9 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
17.3 99.5 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
16.9 99.5 GSM75512 Col-0 0h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
16.5 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.1 99.5 E-ATMX-33-raw-cel-1562596241
15.5 99.5 E-MEXP-828-raw-cel-1156922987
15.4 99.5 E-MEXP-1094-raw-cel-1379507313
14.2 99.4 GSM75517 slr-1 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
13.9 99.4 GSM75513 Col-0 2h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
13.6 99.4 GSM75521 slr-1 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
13.0 99.4 E-MEXP-1094-raw-cel-1379507273
12.6 99.3 E-MEXP-828-raw-cel-1156922968
11.8 99.3 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.8 99.3 GSM75508 Col-0 0h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.7 99.2 E-MEXP-828-raw-cel-1156922485
10.7 99.2 GSM75514 Col-0 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.5 99.2 E-MEXP-828-raw-cel-1156922809
10.3 99.2 GSM75510 Col-0 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
9.8 99.1 GSM142851 MG001_ATH1_A4-Torres-2N1 GSE6176 Impact of Type III effectors on plant defense responses
9.4 99.1 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.4 99.1 GSM75515 Col-0 6h MOCK replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
9.3 99.1 E-MEXP-828-raw-cel-1156922659
9.2 99.1 GSM75518 slr-1 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
140.4	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
108.8	99.9	GSM311274	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
104.9	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
104.7	99.9	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
101.9	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
92.2	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
89.5	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
72.8	99.9	GSM311273	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
68.6	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.7	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.6	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.7	99.7	GSM284385	Arabidopsis GEP6	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
23.5	99.6	GSM75509	Col-0 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
18.0	99.5	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.9	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
17.3	99.5	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
16.9	99.5	GSM75512	Col-0 0h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
16.5	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.1	99.5	E-ATMX-33-raw-cel-1562596241
15.5	99.5	E-MEXP-828-raw-cel-1156922987
15.4	99.5	E-MEXP-1094-raw-cel-1379507313
14.2	99.4	GSM75517	slr-1 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
13.9	99.4	GSM75513	Col-0 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
13.6	99.4	GSM75521	slr-1 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
13.0	99.4	E-MEXP-1094-raw-cel-1379507273
12.6	99.3	E-MEXP-828-raw-cel-1156922968
11.8	99.3	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.8	99.3	GSM75508	Col-0 0h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.7	99.2	E-MEXP-828-raw-cel-1156922485
10.7	99.2	GSM75514	Col-0 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.5	99.2	E-MEXP-828-raw-cel-1156922809
10.3	99.2	GSM75510	Col-0 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.8	99.1	GSM142851	MG001_ATH1_A4-Torres-2N1	GSE6176	Impact of Type III effectors on plant defense responses
9.4	99.1	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.4	99.1	GSM75515	Col-0 6h MOCK replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.3	99.1	E-MEXP-828-raw-cel-1156922659
9.2	99.1	GSM75518	slr-1 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.095 1 GO:0010025 The chemical reactions and pathways resulting in the formation of wax, which includes C16 and C18 fatty acids.
0.038 1 GO:0043086 Any process that stops or reduces the activity of an enzyme.
0.026 2 GO:0009414 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.

SF	Genes	GO ID	Process Name
0.095	1	GO:0010025	The chemical reactions and pathways resulting in the formation of wax, which includes C16 and C18 fatty acids.
0.038	1	GO:0043086	Any process that stops or reduces the activity of an enzyme.
0.026	2	GO:0009414	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG

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

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Gene ID	At5g59320
Gene name	LTP3 (LIPID TRANSFER PROTEIN 3)
Module size	5 genes
NF	0.46
%ile	64.3

Co-expression analysis

Gene ID At5g59320 Gene name LTP3 (LIPID TRANSFER PROTEIN 3) Module size 5 genes NF 0.46 %ile 64.3

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 KEGG

Inter-species module comparison

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

Gene ID At5g59320

Gene name LTP3 (LIPID TRANSFER PROTEIN 3)

Module size 5 genes

NF 0.46

%ile 64.3

: 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

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