CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g30130

Gene name unknown protein

Module size 5 genes

NF 0.58

%ile 79.4

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 At4g30130 829136 unknown protein F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PMF O.I. H.G. S.X.
0.75 86.9 0.84 At1g02800 839385 ATCEL2 Encodes a protein with similarity to endo-1,4-b-glucanases and is a member of Glycoside Hydrolase Family 9. CEL2 is induced by nemotodes and is expressed in syncitia induced by Heterodera schachtii.May be involved in the development and function of syncitia. O.I. H.G. S.X.
0.60 75.7 0.87 At3g06220 819796 DNA binding / transcription factor F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;P O.I. H.G. S.X.
0.57 73.8 0.83 At3g57920 824961 SPL15 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15) Encodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expression is regulated by MIR156b. O.I. H.G. S.X.
0.44 57.2 0.85 At2g42800 818880 AtRLP29 (Receptor Like Protein 29) F:protein binding;P:unknown;C:anchored to membrane, plant-type cell wall;PMOBFA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.	Other DB
0.67	81.6	0.87	At2g42200	818820	SPL9 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9)	Encodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expresssion is regulated by MIR156b.	O.I.	H.G.	S.X.
0.57	73.8	0.81	At3g11000	820271	-	F:unknown;P:unknown;C:endomembrane system;POBFMV	O.I.	H.G.	S.X.
0.57	73.8	0.71	At5g47600	834810	heat shock protein-related	F:molecular_function unknown;P:biological_process unknown;C:unknown;PB	O.I.	H.G.	S.X.
0.55	70.6	0.77	At4g34400	829590	DNA binding / transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:endomembrane system;MOBFPVA	O.I.	H.G.	S.X.
0.47	61.2	0.83	At3g06160	819790	transcriptional factor B3 family protein	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PO	O.I.	H.G.	S.X.
0.46	59.8	0.79	At5g44620	834490	CYP706A3	member of CYP706A	O.I.	H.G.	S.X.
0.40	50.8	0.82	At1g19830	838570	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.40	50.8	0.80	At1g10980	837641	-	F:unknown;P:biological_process unknown;C:vacuole;MFPO	O.I.	H.G.	S.X.
0.40	50.8	0.78	At5g03390	831852	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	H.G.	S.X.
0.40	50.8	0.66	At1g01130	839359	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.36	43.6	0.77	At1g53160	841749	SPL4 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4)	Encodes a member of the SPL (squamosa-promoter binding protein-like)gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. Contains the SBP-box, which encodes the SBP-domain, required and sufficient for interaction with DNA. It is involved in regulation of flowering and vegetative phase change. Its temporal expression is regulated by the microRNA miR156. The target site for the microRNA is in the 3'UTR.	O.I.	H.G.	S.X.
0.33	38.1	0.87	At2g32765	817837	SUMO5 (SMALL UBIQUITINRELATED MODIFIER 5)	Encodes a small ubiquitin-like modifier (SUMO) protein that becomes covalently attached to various intracellular protein targets through an isopeptide bond. SUMOylation typically has a post-translational effect on the behavior of the target protein.	O.I.	H.G.	S.X.
0.29	30.3	0.73	At2g16210	816118	transcriptional factor B3 family protein	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.27	26.2	0.78	At1g24070	839019	ATCSLA10	encodes a gene similar to cellulose synthase	O.I.	H.G.	S.X.
0.27	26.2	0.76	At5g20740	832197	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.26	24.4	0.71	At3g28500	822480	60S acidic ribosomal protein P2 (RPP2C)	F:structural constituent of ribosome;P:translational elongation;C:cytosol, cytosolic ribosome, ribosome, plasma membrane;MFOPAB	O.I.	H.G.	S.X.

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
69.7 99.9 E-MEXP-1725-raw-cel-1669614634
62.8 99.8 E-MEXP-98-raw-cel-320188749
39.6 99.8 E-MEXP-98-raw-cel-320188694
37.1 99.7 E-MEXP-1725-raw-cel-1669614623
27.1 99.7 E-MEXP-98-raw-cel-320188969
20.6 99.6 E-MEXP-1725-raw-cel-1669614562
13.3 99.4 E-ATMX-33-raw-cel-1562596197
12.5 99.3 GSM184911 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
11.8 99.3 E-MEXP-98-raw-cel-320188914
11.0 99.2 E-MEXP-1443-raw-cel-1581869745
10.6 99.2 E-ATMX-33-raw-cel-1562596103
9.8 99.1 E-MEXP-1725-raw-cel-1669614582
9.1 99.1 GSM204069 protoplast_hypoxia_rep1 GSE8248 Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells
8.9 99.0 E-ATMX-33-raw-cel-1562596241

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.222 1 GO:0008361 Any process that modulates the size of a cell.
0.118 1 GO:0007389 Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
0.111 1 GO:0042127 Any process that modulates the frequency, rate or extent of cell proliferation.

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

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