CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g24150

Gene name FH4 (FORMIN HOMOLOGUE 4)

Module size 7 genes

NF 0.43

%ile 60.6

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
0.55 70.6 1.00 At1g24150 839028 FH4 (FORMIN HOMOLOGUE 4) Encodes a group I formin. Localized to cell junctions. Polymerizes actin. Binds profilin. O.I. H.G. S.X.
0.61 76.7 0.86 At4g11850 826791 PLDGAMMA1 phospholipase D (gamma) O.I. H.G. S.X.
0.55 70.6 0.82 At1g18390 838420 ATP binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA O.I. H.G. S.X.
0.50 65.3 0.84 At2g20960 816630 pEARLI4 F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOBPVA O.I. H.G. S.X.
0.35 41.6 0.84 At2g02220 814753 PSKR1 (PHYTOSULFOKIN RECEPTOR 1) Encodes a protein interacting with phytosulfokine, a five amino acid sulfated peptide (YIYTQ). O.I. H.G. S.X.
0.35 41.6 0.82 At1g03740 839423 ATP binding / kinase/ protein kinase/ protein serine/threonine kinase F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:unknown;MPOFBVA O.I. H.G. S.X.
0.27 26.2 0.82 At4g08850 826456 kinase F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane, membrane;MPOBFVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.55	70.6	1.00	At1g24150	839028	FH4 (FORMIN HOMOLOGUE 4)	Encodes a group I formin. Localized to cell junctions. Polymerizes actin. Binds profilin.	O.I.	H.G.	S.X.
0.61	76.7	0.86	At4g11850	826791	PLDGAMMA1	phospholipase D (gamma)	O.I.	H.G.	S.X.
0.55	70.6	0.82	At1g18390	838420	ATP binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase	F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA	O.I.	H.G.	S.X.
0.50	65.3	0.84	At2g20960	816630	pEARLI4	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOBPVA	O.I.	H.G.	S.X.
0.35	41.6	0.84	At2g02220	814753	PSKR1 (PHYTOSULFOKIN RECEPTOR 1)	Encodes a protein interacting with phytosulfokine, a five amino acid sulfated peptide (YIYTQ).	O.I.	H.G.	S.X.
0.35	41.6	0.82	At1g03740	839423	ATP binding / kinase/ protein kinase/ protein serine/threonine kinase	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:unknown;MPOFBVA	O.I.	H.G.	S.X.
0.27	26.2	0.82	At4g08850	826456	kinase	F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane, membrane;MPOBFVA	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
88.9 99.9 GSM133957 Fukuda_1-2_0B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
39.0 99.8 E-MEXP-791-raw-cel-1122937587
33.9 99.7 E-MEXP-791-raw-cel-1122937623
24.2 99.6 GSM131588 ATGE_35_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
22.4 99.6 GSM131590 ATGE_35_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
21.9 99.6 E-MEXP-791-raw-cel-1122937605
20.5 99.6 GSM39200 Col_C2 GSE2169 rre1 and rre2 mutants
20.5 99.6 GSM131589 ATGE_35_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
19.4 99.6 GSM39203 Col_Chitin1 GSE2169 rre1 and rre2 mutants
16.0 99.5 GSM39206 Col_Chitin4 GSE2169 rre1 and rre2 mutants
14.6 99.4 GSM39214 RRE2_Chitin4 GSE2169 rre1 and rre2 mutants
13.2 99.4 GSM39204 Col_Chitin2 GSE2169 rre1 and rre2 mutants
12.5 99.3 GSM39192 RRE1_C2 GSE2169 rre1 and rre2 mutants
12.4 99.3 GSM131578 ATGE_31_C2 GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.5 99.3 GSM39205 Col_Chitin3 GSE2169 rre1 and rre2 mutants
11.3 99.3 GSM131580 ATGE_32_B2 GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.3 99.3 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.2 99.2 GSM131576 ATGE_31_A2 GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.2 99.2 GSM131577 ATGE_31_B2 GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.3 99.2 GSM39201 Col_C3 GSE2169 rre1 and rre2 mutants
10.1 99.2 GSM39208 RRE2_C2 GSE2169 rre1 and rre2 mutants
10.1 99.2 GSM131581 ATGE_32_C2 GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.9 99.1 GSM39199 Col_C1 GSE2169 rre1 and rre2 mutants
9.8 99.1 GSM39191 RRE1_C1 GSE2169 rre1 and rre2 mutants
9.6 99.1 GSM39193 RRE1_C3 GSE2169 rre1 and rre2 mutants
9.1 99.1 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
88.9	99.9	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
39.0	99.8	E-MEXP-791-raw-cel-1122937587
33.9	99.7	E-MEXP-791-raw-cel-1122937623
24.2	99.6	GSM131588	ATGE_35_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
22.4	99.6	GSM131590	ATGE_35_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
21.9	99.6	E-MEXP-791-raw-cel-1122937605
20.5	99.6	GSM39200	Col_C2	GSE2169	rre1 and rre2 mutants
20.5	99.6	GSM131589	ATGE_35_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
19.4	99.6	GSM39203	Col_Chitin1	GSE2169	rre1 and rre2 mutants
16.0	99.5	GSM39206	Col_Chitin4	GSE2169	rre1 and rre2 mutants
14.6	99.4	GSM39214	RRE2_Chitin4	GSE2169	rre1 and rre2 mutants
13.2	99.4	GSM39204	Col_Chitin2	GSE2169	rre1 and rre2 mutants
12.5	99.3	GSM39192	RRE1_C2	GSE2169	rre1 and rre2 mutants
12.4	99.3	GSM131578	ATGE_31_C2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.5	99.3	GSM39205	Col_Chitin3	GSE2169	rre1 and rre2 mutants
11.3	99.3	GSM131580	ATGE_32_B2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.3	99.3	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.2	99.2	GSM131576	ATGE_31_A2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.2	99.2	GSM131577	ATGE_31_B2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.3	99.2	GSM39201	Col_C3	GSE2169	rre1 and rre2 mutants
10.1	99.2	GSM39208	RRE2_C2	GSE2169	rre1 and rre2 mutants
10.1	99.2	GSM131581	ATGE_32_C2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.9	99.1	GSM39199	Col_C1	GSE2169	rre1 and rre2 mutants
9.8	99.1	GSM39191	RRE1_C1	GSE2169	rre1 and rre2 mutants
9.6	99.1	GSM39193	RRE1_C3	GSE2169	rre1 and rre2 mutants
9.1	99.1	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.182 1 GO:0030041 Assembly of actin filaments by the addition of actin monomers to a filament.
0.061 1 GO:0009816 A response of an organism to a bacterium that prevents the occurrence or spread of disease.
0.015 1 GO:0007169 The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

SF	Genes	GO ID	Process Name
0.182	1	GO:0030041	Assembly of actin filaments by the addition of actin monomers to a filament.
0.061	1	GO:0009816	A response of an organism to a bacterium that prevents the occurrence or spread of disease.
0.015	1	GO:0007169	The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.095 1 00565 Ether lipid metabolism
0.054 1 00564 Glycerophospholipid metabolism
0.028 1 04144 Endocytosis

SF	Genes	KEGG ID	Pathway name
0.095	1	00565	Ether lipid metabolism
0.054	1	00564	Glycerophospholipid metabolism
0.028	1	04144	Endocytosis

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	At1g24150
Gene name	FH4 (FORMIN HOMOLOGUE 4)
Module size	7 genes
NF	0.43
%ile	60.6

Co-expression analysis

Gene ID At1g24150 Gene name FH4 (FORMIN HOMOLOGUE 4) Module size 7 genes NF 0.43 %ile 60.6

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 KEGG0.095100565Ether lipid metabolism0.054100564Glycerophospholipid metabolism0.028104144Endocytosis

Inter-species module comparison

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

Gene ID At1g24150

Gene name FH4 (FORMIN HOMOLOGUE 4)

Module size 7 genes

NF 0.43

%ile 60.6

: 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
0.095 1 00565 Ether lipid metabolism
0.054 1 00564 Glycerophospholipid metabolism
0.028 1 04144 Endocytosis

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