CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g38930

Gene name germin-like protein, putative

Module size 12 genes

NF 0.37

%ile 50.0

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
0.26 24.4 1.00 At5g38930 833885 germin-like protein, putative F:manganese ion binding, nutrient reservoir activity;P:biological_process unknown;C:cell wall;PFO O.I. H.G. S.X.
0.53 68.6 0.63 At3g60270 825198 uclacyanin, putative F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;POBVFMA O.I. H.G. S.X.
0.48 62.5 0.55 At4g08380 826395 proline-rich extensin-like family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPFOBVA O.I. H.G. S.X.
0.46 59.8 0.54 At3g05950 819765 germin-like protein, putative F:manganese ion binding, nutrient reservoir activity;P:biological_process unknown;C:endomembrane system, apoplast;PFBO O.I. H.G. S.X.
0.44 57.2 0.60 At1g26250 839166 proline-rich extensin, putative F:structural constituent of cell wall;P:plant-type cell wall organization;C:endomembrane system;MPBOFVA O.I. H.G. S.X.
0.39 48.4 0.53 At5g04730 830351 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.38 46.7 0.52 At1g26240 839165 proline-rich extensin-like family protein F:structural constituent of cell wall;P:plant-type cell wall organization;C:endomembrane system;MPBOFVA O.I. H.G. S.X.
0.38 46.7 0.56 At3g29410 822602 terpene synthase/cyclase family protein F:lyase activity, magnesium ion binding;P:metabolic process;C:unknown;PO O.I. H.G. S.X.
0.38 46.7 0.56 At1g49860 841409 ATGSTF14 Encodes glutathione transferase belonging to the phi class of GSTs. Naming convention according to Wagner et al. (2002). O.I. H.G. S.X.
0.31 33.8 0.55 At1g33840 840280 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF O.I. H.G. S.X.
0.29 30.3 0.61 At4g14630 827113 GLP9 (GERMIN-LIKE PROTEIN 9) germin-like protein with N-terminal signal sequence that may target it to the vacuole, plasma membrane and/or outside the cell. O.I. H.G. S.X.
0.22 17.5 0.65 At5g49770 835040 leucine-rich repeat transmembrane protein kinase, putative F:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;MPOBFVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.26	24.4	1.00	At5g38930	833885	germin-like protein, putative	F:manganese ion binding, nutrient reservoir activity;P:biological_process unknown;C:cell wall;PFO	O.I.	H.G.	S.X.
0.53	68.6	0.63	At3g60270	825198	uclacyanin, putative	F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;POBVFMA	O.I.	H.G.	S.X.
0.48	62.5	0.55	At4g08380	826395	proline-rich extensin-like family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPFOBVA	O.I.	H.G.	S.X.
0.46	59.8	0.54	At3g05950	819765	germin-like protein, putative	F:manganese ion binding, nutrient reservoir activity;P:biological_process unknown;C:endomembrane system, apoplast;PFBO	O.I.	H.G.	S.X.
0.44	57.2	0.60	At1g26250	839166	proline-rich extensin, putative	F:structural constituent of cell wall;P:plant-type cell wall organization;C:endomembrane system;MPBOFVA	O.I.	H.G.	S.X.
0.39	48.4	0.53	At5g04730	830351	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.38	46.7	0.52	At1g26240	839165	proline-rich extensin-like family protein	F:structural constituent of cell wall;P:plant-type cell wall organization;C:endomembrane system;MPBOFVA	O.I.	H.G.	S.X.
0.38	46.7	0.56	At3g29410	822602	terpene synthase/cyclase family protein	F:lyase activity, magnesium ion binding;P:metabolic process;C:unknown;PO	O.I.	H.G.	S.X.
0.38	46.7	0.56	At1g49860	841409	ATGSTF14	Encodes glutathione transferase belonging to the phi class of GSTs. Naming convention according to Wagner et al. (2002).	O.I.	H.G.	S.X.
0.31	33.8	0.55	At1g33840	840280	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.29	30.3	0.61	At4g14630	827113	GLP9 (GERMIN-LIKE PROTEIN 9)	germin-like protein with N-terminal signal sequence that may target it to the vacuole, plasma membrane and/or outside the cell.	O.I.	H.G.	S.X.
0.22	17.5	0.65	At5g49770	835040	leucine-rich repeat transmembrane protein kinase, putative	F:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;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
39.9 99.8 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.3 99.4 GSM154505 Arabidopsis hydrated pollen grains rep1 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
15.1 99.4 E-ATMX-33-raw-cel-1562596310
13.2 99.4 GSM268245 dor-drought-1, biological rep 1 GSE10643 Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
12.7 99.3 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
12.7 99.3 GSM131638 ATGE_73_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
12.5 99.3 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
12.4 99.3 E-ATMX-33-raw-cel-1562596264
12.4 99.3 GSM154506 Arabidopsis hydrated pollen grains rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
11.8 99.3 GSM131637 ATGE_73_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.7 99.3 E-ATMX-35-raw-cel-1574334848
11.5 99.3 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
11.3 99.3 GSM142740 DH001_ATH1_A7-MPG1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
11.0 99.2 GSM151698 gh3.5-1D uninoculated, biological replicate 2 GSE6556 Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2)
10.9 99.2 E-MEXP-1138-raw-cel-1432772970
10.8 99.2 GSM38668 NSNP GSE2268 Arabidopsis polysome microarray
10.8 99.2 E-MEXP-1138-raw-cel-1432772522
10.8 99.2 GSM131636 ATGE_73_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.4 99.2 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.3 99.2 GSM318345 ML_35DAS_2 GSE12676 Arabidopsis thaliana Ler developmental series
10.3 99.2 GSM318332 ML_35DAS_1 GSE12676 Arabidopsis thaliana Ler developmental series
10.1 99.2 E-MEXP-1138-raw-cel-1432772938
10.0 99.2 E-ATMX-35-raw-cel-1574334864
9.7 99.1 E-MEXP-1138-raw-cel-1432772586
9.4 99.1 E-MEXP-285-raw-cel-440782791
9.3 99.1 E-MEXP-1138-raw-cel-1432772682
9.1 99.1 E-MEXP-1138-raw-cel-1432772554
9.0 99.1 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
8.9 99.0 E-MEXP-1138-raw-cel-1432773130
8.9 99.0 GSM154504 Arabidopsis desiccated mature pollen grains rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
8.9 99.0 E-MEXP-1138-raw-cel-1432772746
8.8 99.0 GSM142643 MC002_ATH1_A7.3-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7 99.0 E-MEXP-1138-raw-cel-1432773386
8.6 99.0 E-MEXP-1138-raw-cel-1432772714
8.6 99.0 E-MEXP-1138-raw-cel-1432772618

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
39.9	99.8	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.3	99.4	GSM154505	Arabidopsis hydrated pollen grains rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
15.1	99.4	E-ATMX-33-raw-cel-1562596310
13.2	99.4	GSM268245	dor-drought-1, biological rep 1	GSE10643	Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
12.7	99.3	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
12.7	99.3	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
12.5	99.3	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
12.4	99.3	E-ATMX-33-raw-cel-1562596264
12.4	99.3	GSM154506	Arabidopsis hydrated pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
11.8	99.3	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.7	99.3	E-ATMX-35-raw-cel-1574334848
11.5	99.3	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
11.3	99.3	GSM142740	DH001_ATH1_A7-MPG1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
11.0	99.2	GSM151698	gh3.5-1D uninoculated, biological replicate 2	GSE6556	Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2)
10.9	99.2	E-MEXP-1138-raw-cel-1432772970
10.8	99.2	GSM38668	NSNP	GSE2268	Arabidopsis polysome microarray
10.8	99.2	E-MEXP-1138-raw-cel-1432772522
10.8	99.2	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.4	99.2	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.3	99.2	GSM318345	ML_35DAS_2	GSE12676	Arabidopsis thaliana Ler developmental series
10.3	99.2	GSM318332	ML_35DAS_1	GSE12676	Arabidopsis thaliana Ler developmental series
10.1	99.2	E-MEXP-1138-raw-cel-1432772938
10.0	99.2	E-ATMX-35-raw-cel-1574334864
9.7	99.1	E-MEXP-1138-raw-cel-1432772586
9.4	99.1	E-MEXP-285-raw-cel-440782791
9.3	99.1	E-MEXP-1138-raw-cel-1432772682
9.1	99.1	E-MEXP-1138-raw-cel-1432772554
9.0	99.1	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
8.9	99.0	E-MEXP-1138-raw-cel-1432773130
8.9	99.0	GSM154504	Arabidopsis desiccated mature pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
8.9	99.0	E-MEXP-1138-raw-cel-1432772746
8.8	99.0	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7	99.0	E-MEXP-1138-raw-cel-1432773386
8.6	99.0	E-MEXP-1138-raw-cel-1432772714
8.6	99.0	E-MEXP-1138-raw-cel-1432772618

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.103 2 GO:0009664 A process that results in the assembly and arrangement of constituent parts of the cellulose and pectin-containing cell wall, or in the disassembly of the cellulose and pectin-containing cell wall. This process is carried out at the cellular level. An example of this process is found in Arabidopsis thaliana.
0.034 1 GO:0009407 The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
0.014 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
0.103	2	GO:0009664	A process that results in the assembly and arrangement of constituent parts of the cellulose and pectin-containing cell wall, or in the disassembly of the cellulose and pectin-containing cell wall. This process is carried out at the cellular level. An example of this process is found in Arabidopsis thaliana.
0.034	1	GO:0009407	The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
0.014	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

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	At5g38930
Gene name	germin-like protein, putative
Module size	12 genes
NF	0.37
%ile	50.0

Co-expression analysis

Gene ID At5g38930 Gene name germin-like protein, putative Module size 12 genes NF 0.37 %ile 50.0

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 At5g38930

Gene name germin-like protein, putative

Module size 12 genes

NF 0.37

%ile 50.0

: 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