CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g51590

Gene name LTP12 (LIPID TRANSFER PROTEIN 12)

Module size 5 genes

NF 0.24

%ile 25.3

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
0.17 10.2 1.00 At3g51590 824322 LTP12 (LIPID TRANSFER PROTEIN 12) 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 LTP12 promoter is active exclusively in the tapetum during the uninucleate microspore and bicellular pollen stages. 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 0.78 At4g20420 827790 tapetum-specific protein-related F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.33 38.1 0.78 At3g11980 820372 MS2 (MALE STERILITY 2) Similar to fatty acid reductases. O.I. H.G. S.X.
0.27 26.2 0.78 At4g34850 829637 chalcone and stilbene synthase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, catalytic activity, acyltransferase activity;P:phenylpropanoid biosynthetic process, pollen exine formation;C:cellular_component unknown;PBOF O.I. H.G. S.X.
0.27 26.2 0.79 At1g62940 842596 ACOS5 (ACYL-COA SYNTHETASE 5) encodes an acyl-CoA synthetase, has in vitro activity towards medium- to long-chain fatty acids and their hydroxylated derivatives. Expressed in the tapetum. Involved in pollen wall exine formation. Null mutants were devoid of pollen grains at anther maturity and were completely male sterile. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.17	10.2	1.00	At3g51590	824322	LTP12 (LIPID TRANSFER PROTEIN 12)	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 LTP12 promoter is active exclusively in the tapetum during the uninucleate microspore and bicellular pollen stages. 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	0.78	At4g20420	827790	tapetum-specific protein-related	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.33	38.1	0.78	At3g11980	820372	MS2 (MALE STERILITY 2)	Similar to fatty acid reductases.	O.I.	H.G.	S.X.
0.27	26.2	0.78	At4g34850	829637	chalcone and stilbene synthase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, catalytic activity, acyltransferase activity;P:phenylpropanoid biosynthetic process, pollen exine formation;C:cellular_component unknown;PBOF	O.I.	H.G.	S.X.
0.27	26.2	0.79	At1g62940	842596	ACOS5 (ACYL-COA SYNTHETASE 5)	encodes an acyl-CoA synthetase, has in vitro activity towards medium- to long-chain fatty acids and their hydroxylated derivatives. Expressed in the tapetum. Involved in pollen wall exine formation. Null mutants were devoid of pollen grains at anther maturity and were completely male sterile.	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
27.3 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.7 99.4 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.7 99.4 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
11.7 99.3 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1 99.2 GSM131608 ATGE_42_D GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.0 99.2 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.7 99.2 E-MEXP-509-raw-cel-829148703
10.3 99.2 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0 99.2 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9 99.1 GSM131606 ATGE_42_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.8 99.1 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.3 99.1 GSM131611 ATGE_43_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.1 99.1 GSM131610 ATGE_43_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.0 99.1 GSM131609 ATGE_43_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
8.9 99.0 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.9 99.0 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.9 99.0 GSM131607 ATGE_42_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
8.7 99.0 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.6 99.0 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
27.3	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.7	99.4	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.7	99.4	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
11.7	99.3	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1	99.2	GSM131608	ATGE_42_D	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.0	99.2	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.7	99.2	E-MEXP-509-raw-cel-829148703
10.3	99.2	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9	99.1	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.8	99.1	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.3	99.1	GSM131611	ATGE_43_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.1	99.1	GSM131610	ATGE_43_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.0	99.1	GSM131609	ATGE_43_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
8.9	99.0	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.9	99.0	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.9	99.0	GSM131607	ATGE_42_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
8.7	99.0	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.6	99.0	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0046949 The chemical reactions and pathways resulting in the formation of acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty-acyl group.
0.316 3 GO:0010584 The formation of the pollen exine. The reticulate pollen wall pattern consists of two layers, exine and intine.
0.250 1 GO:0080110 The chemical reactions and pathways resulting in the formation of sporopollenin, a primary constituent of the pollen exine layer.

SF	Genes	GO ID	Process Name
0.333	1	GO:0046949	The chemical reactions and pathways resulting in the formation of acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty-acyl group.
0.316	3	GO:0010584	The formation of the pollen exine. The reticulate pollen wall pattern consists of two layers, exine and intine.
0.250	1	GO:0080110	The chemical reactions and pathways resulting in the formation of sporopollenin, a primary constituent of the pollen exine layer.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.067 1 00130 Ubiquinone and other terpenoid-quinone biosynthesis
0.019 1 00940 Phenylpropanoid biosynthesis
0.011 1 01063 Biosynthesis of alkaloids derived from shikimate pathway

SF	Genes	KEGG ID	Pathway name
0.067	1	00130	Ubiquinone and other terpenoid-quinone biosynthesis
0.019	1	00940	Phenylpropanoid biosynthesis
0.011	1	01063	Biosynthesis of alkaloids derived from shikimate pathway

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	At3g51590
Gene name	LTP12 (LIPID TRANSFER PROTEIN 12)
Module size	5 genes
NF	0.24
%ile	25.3

Co-expression analysis

Gene ID At3g51590 Gene name LTP12 (LIPID TRANSFER PROTEIN 12) Module size 5 genes NF 0.24 %ile 25.3

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 KEGG0.067100130Ubiquinone and other terpenoid-quinone biosynthesis0.019100940Phenylpropanoid biosynthesis0.011101063Biosynthesis of alkaloids derived from shikimate pathway

Inter-species module comparison

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

Gene ID At3g51590

Gene name LTP12 (LIPID TRANSFER PROTEIN 12)

Module size 5 genes

NF 0.24

%ile 25.3

: 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
0.067 1 00130 Ubiquinone and other terpenoid-quinone biosynthesis
0.019 1 00940 Phenylpropanoid biosynthesis
0.011 1 01063 Biosynthesis of alkaloids derived from shikimate pathway

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