CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g62360

Gene name invertase/pectin methylesterase inhibitor family protein

Module size 5 genes

NF 0.05

%ile 3.1

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
0.17 10.2 1.00 At5g62360 836357 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:cellular_component unknown;PFO O.I. H.G. S.X.
0.33 38.1 0.61 At1g11210 837662 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:endomembrane system;PO O.I. H.G. S.X.
0.13 5.8 0.65 At5g24470 832518 APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5) Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light. O.I. H.G. S.X.
0.05 1.1 0.63 At4g32800 829416 AP2 domain-containing transcription factor TINY, putative encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY. O.I. H.G. S.X.
0.03 0.6 0.64 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.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.17	10.2	1.00	At5g62360	836357	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:cellular_component unknown;PFO	O.I.	H.G.	S.X.
0.33	38.1	0.61	At1g11210	837662	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:endomembrane system;PO	O.I.	H.G.	S.X.
0.13	5.8	0.65	At5g24470	832518	APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5)	Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light.	O.I.	H.G.	S.X.
0.05	1.1	0.63	At4g32800	829416	AP2 domain-containing transcription factor TINY, putative	encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.	O.I.	H.G.	S.X.
0.03	0.6	0.64	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.

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
41.5 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
33.3 99.7 GSM297382 At.StarchSD.WTSS3.SS3R1L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
23.4 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.2 99.6 GSM297392 At.StarchSD.WTSS3.WTR1L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
18.5 99.5 GSM297387 At.StarchSD.WTSS3.SS3R2L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
17.8 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.6 99.5 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.4 99.5 GSM297397 At.StarchSD.WTSS3.WTR2L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
15.9 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.7 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.6 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1 99.4 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.6 99.4 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8 99.4 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 GSM142853 MG001_ATH1_A6-Torres-2N6 GSE6176 Impact of Type III effectors on plant defense responses
13.1 99.4 GSM142839 MG001_ATH1_A18-Torres-6N6 GSE6176 Impact of Type III effectors on plant defense responses
13.0 99.4 GSM142829 GM001_ATH1_A11-Torres-5N3 GSE6176 Impact of Type III effectors on plant defense responses
12.8 99.3 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7 99.3 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.5 99.3 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5 99.3 GSM38668 NSNP GSE2268 Arabidopsis polysome microarray
10.8 99.2 GSM131127 AtGen_B-13_1-6-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.7 99.2 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.6 99.2 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
10.4 99.2 GSM131139 AtGen_B-25_2-4-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.3 99.2 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.1 99.2 GSM131111 AtGen_B-39_3-4-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.0 99.2 GSM38669 NSPS GSE2268 Arabidopsis polysome microarray
9.7 99.1 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.7 99.1 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4 99.1 GSM38670 DSNP GSE2268 Arabidopsis polysome microarray
9.2 99.1 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1 99.1 GSM131113 AtGen_B-41_3-6-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.0 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8 99.0 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
8.8 99.0 GSM38671 DSPS GSE2268 Arabidopsis polysome microarray
8.7 99.0 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.6 99.0 GSM142852 MG001_ATH1_A5-Torres-2N3 GSE6176 Impact of Type III effectors on plant defense responses

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
41.5	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
33.3	99.7	GSM297382	At.StarchSD.WTSS3.SS3R1L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
23.4	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.2	99.6	GSM297392	At.StarchSD.WTSS3.WTR1L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
18.5	99.5	GSM297387	At.StarchSD.WTSS3.SS3R2L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
17.8	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.6	99.5	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.4	99.5	GSM297397	At.StarchSD.WTSS3.WTR2L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
15.9	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.7	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.6	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.6	99.4	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8	99.4	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	GSM142853	MG001_ATH1_A6-Torres-2N6	GSE6176	Impact of Type III effectors on plant defense responses
13.1	99.4	GSM142839	MG001_ATH1_A18-Torres-6N6	GSE6176	Impact of Type III effectors on plant defense responses
13.0	99.4	GSM142829	GM001_ATH1_A11-Torres-5N3	GSE6176	Impact of Type III effectors on plant defense responses
12.8	99.3	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7	99.3	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.5	99.3	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5	99.3	GSM38668	NSNP	GSE2268	Arabidopsis polysome microarray
10.8	99.2	GSM131127	AtGen_B-13_1-6-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.7	99.2	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.6	99.2	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
10.4	99.2	GSM131139	AtGen_B-25_2-4-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.3	99.2	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.1	99.2	GSM131111	AtGen_B-39_3-4-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.0	99.2	GSM38669	NSPS	GSE2268	Arabidopsis polysome microarray
9.7	99.1	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.7	99.1	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4	99.1	GSM38670	DSNP	GSE2268	Arabidopsis polysome microarray
9.2	99.1	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1	99.1	GSM131113	AtGen_B-41_3-6-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.0	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8	99.0	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
8.8	99.0	GSM38671	DSPS	GSE2268	Arabidopsis polysome microarray
8.7	99.0	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.6	99.0	GSM142852	MG001_ATH1_A5-Torres-2N3	GSE6176	Impact of Type III effectors on plant defense responses

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.051 1 GO:0007623 Any biological process in an organism that recurs with a regularity of approximately 24 hours.
0.044 1 GO:0009640 The control of plant growth, development, and differentiation by the duration and nature of light, independent of photosynthesis.
0.044 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
0.051	1	GO:0007623	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
0.044	1	GO:0009640	The control of plant growth, development, and differentiation by the duration and nature of light, independent of photosynthesis.
0.044	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
0.059 1 04712 Circadian rhythm - plant

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.059	1	04712	Circadian rhythm - plant

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	At5g62360
Gene name	invertase/pectin methylesterase inhibitor family protein
Module size	5 genes
NF	0.05
%ile	3.1

Co-expression analysis

Gene ID At5g62360 Gene name invertase/pectin methylesterase inhibitor family protein Module size 5 genes NF 0.05 %ile 3.1

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 KEGG0.059104712Circadian rhythm - plant

Inter-species module comparison

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

Gene ID At5g62360

Gene name invertase/pectin methylesterase inhibitor family protein

Module size 5 genes

NF 0.05

%ile 3.1

: 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
0.059 1 04712 Circadian rhythm - plant

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