CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g26740

Gene name CCL (CCR-LIKE)

Module size 5 genes

NF 0.70

%ile 88.7

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 At3g26740 822286 CCL (CCR-LIKE) transcripts are differentially regulated at the level of mRNA stability at different times of day controlled by the circadian clock. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. O.I. H.G. S.X.
0.89 94.6 0.90 At4g32340 829368 - F:unknown;P:unknown;C:unknown;MPBOFVA O.I. H.G. S.X.
0.67 81.6 0.90 At1g06460 837158 ACD32.1 (ALPHA-CRYSTALLIN DOMAIN 32.1) ACD32.1 encodes an alpha-crystallin domain containing protein with homology to small heat shock proteins. O.I. H.G. S.X.
0.53 68.6 0.91 At5g06690 830558 WCRKC1 (WCRKC THIOREDOXIN 1) Encodes a thioredoxin (WCRKC1) localized in chloroplast stroma. Contains a WCRKC motif. O.I. H.G. S.X.
0.40 50.8 0.91 At3g15840 820827 PIFI (post-illumination chlorophyll fluorescence increase) Encodes a chloroplast-targeted protein localized in the stroma that is a novel component essential for NDH-mediated non-photochemical reduction of the plastoquinone pool in chlororespiratory electron transport. 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	At3g26740	822286	CCL (CCR-LIKE)	transcripts are differentially regulated at the level of mRNA stability at different times of day controlled by the circadian clock. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant.	O.I.	H.G.	S.X.
0.89	94.6	0.90	At4g32340	829368	-	F:unknown;P:unknown;C:unknown;MPBOFVA	O.I.	H.G.	S.X.
0.67	81.6	0.90	At1g06460	837158	ACD32.1 (ALPHA-CRYSTALLIN DOMAIN 32.1)	ACD32.1 encodes an alpha-crystallin domain containing protein with homology to small heat shock proteins.	O.I.	H.G.	S.X.
0.53	68.6	0.91	At5g06690	830558	WCRKC1 (WCRKC THIOREDOXIN 1)	Encodes a thioredoxin (WCRKC1) localized in chloroplast stroma. Contains a WCRKC motif.	O.I.	H.G.	S.X.
0.40	50.8	0.91	At3g15840	820827	PIFI (post-illumination chlorophyll fluorescence increase)	Encodes a chloroplast-targeted protein localized in the stroma that is a novel component essential for NDH-mediated non-photochemical reduction of the plastoquinone pool in chlororespiratory electron transport.	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
66.5 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.0 99.8 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
64.1 99.8 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
59.2 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.7 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.6 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
48.0 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.0 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.5 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.8 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.4 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.9 99.7 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
28.2 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.4 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.6 99.6 E-MEXP-509-raw-cel-829148525
24.2 99.6 E-MEXP-509-raw-cel-829148597
24.1 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.0 99.6 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
23.4 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.2 99.6 E-MEXP-509-raw-cel-829148561
20.5 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
17.3 99.5 E-MEXP-1443-raw-cel-1581869803
15.5 99.5 GSM284391 Arabidopsis GPE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
15.2 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.1 99.4 E-MEXP-1443-raw-cel-1581869745
14.3 99.4 E-MEXP-509-raw-cel-829148129
12.9 99.3 E-MEXP-509-raw-cel-829148492
12.9 99.3 E-MEXP-509-raw-cel-829148420
12.4 99.3 E-MEXP-509-raw-cel-829148313
12.1 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.6 99.3 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.4 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.3 99.3 E-MEXP-509-raw-cel-829148913
11.2 99.2 E-MEXP-509-raw-cel-829148456
11.2 99.2 E-MEXP-1443-raw-cel-1581869921
11.0 99.2 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.9 99.2 E-MEXP-509-raw-cel-829148348
10.2 99.2 GSM75509 Col-0 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.1 99.2 E-MEXP-509-raw-cel-829148666
10.1 99.2 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.9 99.1 E-MEXP-509-raw-cel-829148201
9.8 99.1 GSM204069 protoplast_hypoxia_rep1 GSE8248 Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells
9.5 99.1 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 E-MEXP-509-raw-cel-829148385
9.3 99.1 E-MEXP-509-raw-cel-829148165
9.0 99.1 GSM205156 protoplast_controlDNA_rep1 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
9.0 99.1 GSM75520 slr-1 2h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
8.8 99.0 E-MEXP-509-raw-cel-829148090
8.7 99.0 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7 99.0 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.6 99.0 E-MEXP-509-raw-cel-829148632
8.6 99.0 GSM133958 Fukuda_1-3_2A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.6 99.0 GSM75517 slr-1 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
66.5	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.0	99.8	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
64.1	99.8	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
59.2	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.7	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.6	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
48.0	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.0	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.5	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.8	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.4	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.9	99.7	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
28.2	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.4	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.6	99.6	E-MEXP-509-raw-cel-829148525
24.2	99.6	E-MEXP-509-raw-cel-829148597
24.1	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.0	99.6	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
23.4	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.2	99.6	E-MEXP-509-raw-cel-829148561
20.5	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
17.3	99.5	E-MEXP-1443-raw-cel-1581869803
15.5	99.5	GSM284391	Arabidopsis GPE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
15.2	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.1	99.4	E-MEXP-1443-raw-cel-1581869745
14.3	99.4	E-MEXP-509-raw-cel-829148129
12.9	99.3	E-MEXP-509-raw-cel-829148492
12.9	99.3	E-MEXP-509-raw-cel-829148420
12.4	99.3	E-MEXP-509-raw-cel-829148313
12.1	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.6	99.3	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.4	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.3	99.3	E-MEXP-509-raw-cel-829148913
11.2	99.2	E-MEXP-509-raw-cel-829148456
11.2	99.2	E-MEXP-1443-raw-cel-1581869921
11.0	99.2	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.9	99.2	E-MEXP-509-raw-cel-829148348
10.2	99.2	GSM75509	Col-0 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.1	99.2	E-MEXP-509-raw-cel-829148666
10.1	99.2	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.9	99.1	E-MEXP-509-raw-cel-829148201
9.8	99.1	GSM204069	protoplast_hypoxia_rep1	GSE8248	Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells
9.5	99.1	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	E-MEXP-509-raw-cel-829148385
9.3	99.1	E-MEXP-509-raw-cel-829148165
9.0	99.1	GSM205156	protoplast_controlDNA_rep1	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
9.0	99.1	GSM75520	slr-1 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.8	99.0	E-MEXP-509-raw-cel-829148090
8.7	99.0	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7	99.0	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.6	99.0	E-MEXP-509-raw-cel-829148632
8.6	99.0	GSM133958	Fukuda_1-3_2A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.6	99.0	GSM75517	slr-1 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0010478 A respiratory electron flow (from NAD(P)H to plastoquinone (PQ) and O2) involving both a nonphotochemical reduction and re-oxidation of PQ pool.
0.019 1 GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.
0.017 1 GO:0009408 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 a heat stimulus, a temperature stimulus above the optimal temperature for that organism.

SF	Genes	GO ID	Process Name
0.333	1	GO:0010478	A respiratory electron flow (from NAD(P)H to plastoquinone (PQ) and O2) involving both a nonphotochemical reduction and re-oxidation of PQ pool.
0.019	1	GO:0045454	Any process that maintains the redox environment of a cell or compartment within a cell.
0.017	1	GO:0009408	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 a heat stimulus, a temperature stimulus above the optimal temperature for that organism.

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	At3g26740
Gene name	CCL (CCR-LIKE)
Module size	5 genes
NF	0.70
%ile	88.7

Co-expression analysis

Gene ID At3g26740 Gene name CCL (CCR-LIKE) Module size 5 genes NF 0.70 %ile 88.7

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 At3g26740

Gene name CCL (CCR-LIKE)

Module size 5 genes

NF 0.70

%ile 88.7

: 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