CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g62280

Gene name unknown protein

Module size 9 genes

NF 0.33

%ile 42.3

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
0.43 55.3 1.00 At5g62280 836349 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.50 65.3 0.80 At5g02760 831234 protein phosphatase 2C family protein / PP2C family protein F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;PMOFBAV O.I. H.G. S.X.
0.40 50.8 0.59 At2g18010 816313 auxin-responsive family protein F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. H.G. S.X.
0.40 50.8 0.62 At4g34770 829629 auxin-responsive family protein F:unknown;P:response to auxin stimulus;C:unknown;PO O.I. H.G. S.X.
0.33 38.1 0.69 At4g32280 829361 IAA29 (INDOLE-3-ACETIC ACID INDUCIBLE 29) Auxin inducible protein. O.I. H.G. S.X.
0.27 26.2 0.61 At4g14130 827051 XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7) xyloglucan endotransglycosylase-related protein (XTR7) O.I. H.G. S.X.
0.27 26.2 0.62 At5g57240 835830 ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C) F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP O.I. H.G. S.X.
0.22 17.5 0.60 At4g16515 827350 unknown protein F:molecular_function unknown;P:unknown;C:endomembrane system;P O.I. H.G. S.X.
0.20 14.4 0.63 At1g67910 843119 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.43	55.3	1.00	At5g62280	836349	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.50	65.3	0.80	At5g02760	831234	protein phosphatase 2C family protein / PP2C family protein	F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;PMOFBAV	O.I.	H.G.	S.X.
0.40	50.8	0.59	At2g18010	816313	auxin-responsive family protein	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.40	50.8	0.62	At4g34770	829629	auxin-responsive family protein	F:unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.33	38.1	0.69	At4g32280	829361	IAA29 (INDOLE-3-ACETIC ACID INDUCIBLE 29)	Auxin inducible protein.	O.I.	H.G.	S.X.
0.27	26.2	0.61	At4g14130	827051	XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7)	xyloglucan endotransglycosylase-related protein (XTR7)	O.I.	H.G.	S.X.
0.27	26.2	0.62	At5g57240	835830	ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C)	F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.
0.22	17.5	0.60	At4g16515	827350	unknown protein	F:molecular_function unknown;P:unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.20	14.4	0.63	At1g67910	843119	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	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
39.1 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.8 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.1 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.5 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.8 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.0 99.7 E-MEXP-285-raw-cel-440782725
23.7 99.6 E-MEXP-1138-raw-cel-1432773322
23.3 99.6 E-MEXP-1138-raw-cel-1432773258
22.3 99.6 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
22.2 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2 99.6 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
21.1 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.7 99.6 GSM131638 ATGE_73_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
20.6 99.6 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
19.8 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.5 99.6 GSM131637 ATGE_73_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
19.1 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.0 99.5 E-MEXP-1138-raw-cel-1432773290
18.9 99.5 E-MEXP-1138-raw-cel-1432773066
18.4 99.5 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2 99.5 GSM142740 DH001_ATH1_A7-MPG1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
18.0 99.5 E-MEXP-285-raw-cel-440782791
17.9 99.5 E-MEXP-1138-raw-cel-1432772938
17.5 99.5 E-MEXP-1138-raw-cel-1432772906
17.1 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.1 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1 99.5 GSM131636 ATGE_73_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
16.9 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.7 99.5 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.8 99.5 GSM133302 NO.27 GSE5699 AtGenExpress: ARR21C overexpression
15.1 99.4 GSM133300 NO.25 GSE5699 AtGenExpress: ARR21C overexpression
14.7 99.4 GSM133301 NO.26 GSE5699 AtGenExpress: ARR21C overexpression
14.6 99.4 E-MEXP-1138-raw-cel-1432772810
14.4 99.4 E-MEXP-1138-raw-cel-1432772714
14.2 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.0 99.4 E-MEXP-1138-raw-cel-1432773034
13.1 99.4 E-ATMX-35-raw-cel-1574334880
13.0 99.4 E-MEXP-1138-raw-cel-1432772842
13.0 99.4 E-MEXP-1138-raw-cel-1432773354
12.7 99.3 E-MEXP-1138-raw-cel-1432772522
12.6 99.3 E-MEXP-1138-raw-cel-1432772874
12.4 99.3 E-MEXP-1138-raw-cel-1432772746
12.4 99.3 E-MEXP-1138-raw-cel-1432772682
12.0 99.3 E-MEXP-1138-raw-cel-1432772778
11.8 99.3 E-MEXP-1138-raw-cel-1432772650
11.6 99.3 GSM133821 Yang_1-6_old-pod_Rep3_ATH1 GSE5736 To identify changes in gene expression during silique senescence in Arabidopsis thaliana
11.5 99.3 E-ATMX-35-raw-cel-1574334864
10.7 99.2 GSM154504 Arabidopsis desiccated mature pollen grains rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
10.5 99.2 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.4 99.2 E-MEXP-1138-raw-cel-1432773194
10.3 99.2 GSM154506 Arabidopsis hydrated pollen grains rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
10.2 99.2 E-MEXP-1138-raw-cel-1432772586
10.1 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.8 99.1 GSM154505 Arabidopsis hydrated pollen grains rep1 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
9.8 99.1 E-MEXP-1138-raw-cel-1432773130
9.4 99.1 E-MEXP-1138-raw-cel-1432773226
9.2 99.1 E-MEXP-1138-raw-cel-1432773002
9.1 99.1 E-MEXP-1138-raw-cel-1432773162
9.1 99.1 E-MEXP-1138-raw-cel-1432772618
8.9 99.0 E-MEXP-1138-raw-cel-1432772970
8.6 99.0 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
39.1	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.8	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.1	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.5	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.8	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.0	99.7	E-MEXP-285-raw-cel-440782725
23.7	99.6	E-MEXP-1138-raw-cel-1432773322
23.3	99.6	E-MEXP-1138-raw-cel-1432773258
22.3	99.6	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
22.2	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2	99.6	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
21.1	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.7	99.6	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
20.6	99.6	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
19.8	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.5	99.6	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
19.1	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.0	99.5	E-MEXP-1138-raw-cel-1432773290
18.9	99.5	E-MEXP-1138-raw-cel-1432773066
18.4	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2	99.5	GSM142740	DH001_ATH1_A7-MPG1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
18.0	99.5	E-MEXP-285-raw-cel-440782791
17.9	99.5	E-MEXP-1138-raw-cel-1432772938
17.5	99.5	E-MEXP-1138-raw-cel-1432772906
17.1	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.1	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1	99.5	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.9	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.7	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.8	99.5	GSM133302	NO.27	GSE5699	AtGenExpress: ARR21C overexpression
15.1	99.4	GSM133300	NO.25	GSE5699	AtGenExpress: ARR21C overexpression
14.7	99.4	GSM133301	NO.26	GSE5699	AtGenExpress: ARR21C overexpression
14.6	99.4	E-MEXP-1138-raw-cel-1432772810
14.4	99.4	E-MEXP-1138-raw-cel-1432772714
14.2	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.0	99.4	E-MEXP-1138-raw-cel-1432773034
13.1	99.4	E-ATMX-35-raw-cel-1574334880
13.0	99.4	E-MEXP-1138-raw-cel-1432772842
13.0	99.4	E-MEXP-1138-raw-cel-1432773354
12.7	99.3	E-MEXP-1138-raw-cel-1432772522
12.6	99.3	E-MEXP-1138-raw-cel-1432772874
12.4	99.3	E-MEXP-1138-raw-cel-1432772746
12.4	99.3	E-MEXP-1138-raw-cel-1432772682
12.0	99.3	E-MEXP-1138-raw-cel-1432772778
11.8	99.3	E-MEXP-1138-raw-cel-1432772650
11.6	99.3	GSM133821	Yang_1-6_old-pod_Rep3_ATH1	GSE5736	To identify changes in gene expression during silique senescence in Arabidopsis thaliana
11.5	99.3	E-ATMX-35-raw-cel-1574334864
10.7	99.2	GSM154504	Arabidopsis desiccated mature pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
10.5	99.2	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.4	99.2	E-MEXP-1138-raw-cel-1432773194
10.3	99.2	GSM154506	Arabidopsis hydrated pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
10.2	99.2	E-MEXP-1138-raw-cel-1432772586
10.1	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.8	99.1	GSM154505	Arabidopsis hydrated pollen grains rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
9.8	99.1	E-MEXP-1138-raw-cel-1432773130
9.4	99.1	E-MEXP-1138-raw-cel-1432773226
9.2	99.1	E-MEXP-1138-raw-cel-1432773002
9.1	99.1	E-MEXP-1138-raw-cel-1432773162
9.1	99.1	E-MEXP-1138-raw-cel-1432772618
8.9	99.0	E-MEXP-1138-raw-cel-1432772970
8.6	99.0	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.095 1 GO:0008202 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
0.065 1 GO:0006073 The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.041 1 GO:0010218 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 far red light stimulus. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.

SF	Genes	GO ID	Process Name
0.095	1	GO:0008202	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
0.065	1	GO:0006073	The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.041	1	GO:0010218	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 far red light stimulus. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.

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	At5g62280
Gene name	unknown protein
Module size	9 genes
NF	0.33
%ile	42.3

Co-expression analysis

Gene ID At5g62280 Gene name unknown protein Module size 9 genes NF 0.33 %ile 42.3

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 At5g62280

Gene name unknown protein

Module size 9 genes

NF 0.33

%ile 42.3

: 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