CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g42540

Gene name COR15A (COLD-REGULATED 15A)

Module size 5 genes

NF 0.67

%ile 86.9

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
1.00 100.0 1.00 At2g42540 818854 COR15A (COLD-REGULATED 15A) A cold-regulated gene whose product is targeted to the chloroplast and constitutive expression increases freezing tolerance in protoplasts in vitro and chloroplasts in vivo. NMR and x-ray diffraction studies suggest that COR15a alters the intrinsic curvature of the inner membrane of chloroplast envelope. O.I. H.G. S.X.
0.80 89.8 0.88 At2g42530 818853 COR15B (COLD REGULATED 15B) F:unknown;P:response to cold;C:chloroplast, chloroplast stroma, chloroplast envelope;PBOMF O.I. H.G. S.X.
0.67 81.6 0.82 At5g15960 831453 KIN1 cold and ABA inducible protein kin1, possibly functions as an anti-freeze protein. Transcript level of this gene is induced by cold, ABA, dehydration and osmoticum (mannitol). However, protein activity of GUS fused to the promoter of this gene is inhibited by cold treatment, suggesting an inhibition of the protein by increased transcript level. O.I. H.G. S.X.
0.50 65.3 0.79 At1g29395 839815 COR414-TM1 encodes a protein similar to the cold acclimation protein WCOR413 in wheat. Expression is induced by short-term cold-treatment, water deprivation, and abscisic acid treatment. Possibly targeted to thylakoid membrane. O.I. H.G. S.X.
0.44 57.2 0.80 At4g30650 829188 hydrophobic protein, putative / low temperature and salt responsive protein, putative F:unknown;P:response to salt stress, hyperosmotic salinity response, response to cold;C:endomembrane system, integral to membrane;BFPMO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At2g42540	818854	COR15A (COLD-REGULATED 15A)	A cold-regulated gene whose product is targeted to the chloroplast and constitutive expression increases freezing tolerance in protoplasts in vitro and chloroplasts in vivo. NMR and x-ray diffraction studies suggest that COR15a alters the intrinsic curvature of the inner membrane of chloroplast envelope.	O.I.	H.G.	S.X.
0.80	89.8	0.88	At2g42530	818853	COR15B (COLD REGULATED 15B)	F:unknown;P:response to cold;C:chloroplast, chloroplast stroma, chloroplast envelope;PBOMF	O.I.	H.G.	S.X.
0.67	81.6	0.82	At5g15960	831453	KIN1	cold and ABA inducible protein kin1, possibly functions as an anti-freeze protein. Transcript level of this gene is induced by cold, ABA, dehydration and osmoticum (mannitol). However, protein activity of GUS fused to the promoter of this gene is inhibited by cold treatment, suggesting an inhibition of the protein by increased transcript level.	O.I.	H.G.	S.X.
0.50	65.3	0.79	At1g29395	839815	COR414-TM1	encodes a protein similar to the cold acclimation protein WCOR413 in wheat. Expression is induced by short-term cold-treatment, water deprivation, and abscisic acid treatment. Possibly targeted to thylakoid membrane.	O.I.	H.G.	S.X.
0.44	57.2	0.80	At4g30650	829188	hydrophobic protein, putative / low temperature and salt responsive protein, putative	F:unknown;P:response to salt stress, hyperosmotic salinity response, response to cold;C:endomembrane system, integral to membrane;BFPMO	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
245.8 100.0 GSM284394 Arabidopsis GCE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
193.9 100.0 GSM284392 Arabidopsis GCE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
173.2 100.0 GSM311280 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
171.4 100.0 GSM284393 Arabidopsis GCE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
118.7 99.9 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
116.0 99.9 GSM311279 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
79.3 99.9 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
76.9 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
73.6 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.4 99.9 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.1 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.9 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.5 99.9 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.3 99.8 E-MEXP-1474-raw-cel-1593932865
64.3 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.2 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.1 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5 99.8 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
56.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.2 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.8 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.4 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.5 99.8 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
45.9 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.2 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.3 99.8 E-MEXP-1474-raw-cel-1593932929
36.2 99.7 E-MEXP-1474-raw-cel-1593932801
26.3 99.7 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
25.9 99.7 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.7 99.6 E-MEXP-1451-raw-cel-1585200362
17.5 99.5 GSM189112 HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1 GSE7796 Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
16.5 99.5 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.5 99.2 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
9.4 99.1 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
9.1 99.1 E-MEXP-265-raw-cel-414618394

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
245.8	100.0	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
193.9	100.0	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
173.2	100.0	GSM311280	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
171.4	100.0	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
118.7	99.9	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
116.0	99.9	GSM311279	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
79.3	99.9	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
76.9	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
73.6	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.4	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.1	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.9	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.5	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.3	99.8	E-MEXP-1474-raw-cel-1593932865
64.3	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.2	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.1	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5	99.8	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
56.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.2	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.8	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.4	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.5	99.8	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
45.9	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.2	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.3	99.8	E-MEXP-1474-raw-cel-1593932929
36.2	99.7	E-MEXP-1474-raw-cel-1593932801
26.3	99.7	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
25.9	99.7	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.7	99.6	E-MEXP-1451-raw-cel-1585200362
17.5	99.5	GSM189112	HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1	GSE7796	Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
16.5	99.5	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.5	99.2	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
9.4	99.1	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
9.1	99.1	E-MEXP-265-raw-cel-414618394

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.240 3 GO:0009631 Any process that increases freezing tolerance of an organism in response to low, nonfreezing temperatures.
0.200 1 GO:0042631 A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of water.
0.143 2 GO:0010017 The series of molecular signals initiated upon sensing by photoreceptor molecules of red light or far red light. Red light is electromagnetic radiation of wavelength of 580-700nm. 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
0.240	3	GO:0009631	Any process that increases freezing tolerance of an organism in response to low, nonfreezing temperatures.
0.200	1	GO:0042631	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of water.
0.143	2	GO:0010017	The series of molecular signals initiated upon sensing by photoreceptor molecules of red light or far red light. Red light is electromagnetic radiation of wavelength of 580-700nm. 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

Back to the KAGIANA project homepage

Gene ID	At2g42540
Gene name	COR15A (COLD-REGULATED 15A)
Module size	5 genes
NF	0.67
%ile	86.9

Co-expression analysis

Gene ID At2g42540 Gene name COR15A (COLD-REGULATED 15A) Module size 5 genes NF 0.67 %ile 86.9

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 At2g42540

Gene name COR15A (COLD-REGULATED 15A)

Module size 5 genes

NF 0.67

%ile 86.9

: 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