CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g08030

Gene name unknown protein

Module size 12 genes

NF 0.16

%ile 12.9

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 At3g08030 819994 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cell wall;PB O.I. H.G. S.X.
0.35 41.6 0.85 At3g13920 820605 EIF4A1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 4A1) eukaryotic translation initiation factor 4A-1 O.I. H.G. S.X.
0.31 33.8 0.86 At2g39990 818587 EIF2 translation initiation factor eIF2 p47 subunit homolog O.I. H.G. S.X.
0.27 26.2 0.85 At5g45620 834602 26S proteasome regulatory subunit, putative (RPN9) F:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:proteasome regulatory particle, lid subcomplex;MFOP O.I. H.G. S.X.
0.25 22.6 0.85 At4g33250 829461 EIF3K (EUKARYOTIC TRANSLATION INITIATION FACTOR 3K) Encodes initiation factor 3k (EIF3k). O.I. H.G. S.X.
0.20 14.4 0.86 At4g14000 827036 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOPB O.I. H.G. S.X.
0.19 12.7 0.85 At5g38480 833836 GRF3 (GENERAL REGULATORY FACTOR 3) general regulatory factor, a 14-3-3 gene O.I. H.G. S.X.
0.18 11.4 0.85 At1g18080 838388 ATARCA Encodes the Arabidopsis thaliana homolog of the tobacco WD-40 repeat ArcA gene. O.I. H.G. S.X.
0.15 7.8 0.85 At3g57290 824896 EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E) Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation. O.I. H.G. S.X.
0.14 6.8 0.86 At4g00100 828167 ATRPS13A (ARABIDOPSIS THALIANA RIBOSOMAL PROTEIN S13A) Encodes a cytoplasmic ribosomal protein S13 homologue involved in early leaf development O.I. H.G. S.X.
0.11 4.1 0.85 At2g27530 817299 PGY1 (PIGGYBACK1) Encodes ribosomal protein L10aP. Identified in a screen for enhancers of as1. as1/pgy double mutants show defects in leaf vascular patterning and adaxial cell fate. Double mutant analysis indicates pgy genes function in the same pathway as REV, KAN1 and KAN2. O.I. H.G. S.X.
0.05 1.1 0.86 At3g14860 820715 NHL repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPAM 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	At3g08030	819994	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cell wall;PB	O.I.	H.G.	S.X.
0.35	41.6	0.85	At3g13920	820605	EIF4A1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 4A1)	eukaryotic translation initiation factor 4A-1	O.I.	H.G.	S.X.
0.31	33.8	0.86	At2g39990	818587	EIF2	translation initiation factor eIF2 p47 subunit homolog	O.I.	H.G.	S.X.
0.27	26.2	0.85	At5g45620	834602	26S proteasome regulatory subunit, putative (RPN9)	F:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:proteasome regulatory particle, lid subcomplex;MFOP	O.I.	H.G.	S.X.
0.25	22.6	0.85	At4g33250	829461	EIF3K (EUKARYOTIC TRANSLATION INITIATION FACTOR 3K)	Encodes initiation factor 3k (EIF3k).	O.I.	H.G.	S.X.
0.20	14.4	0.86	At4g14000	827036	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOPB	O.I.	H.G.	S.X.
0.19	12.7	0.85	At5g38480	833836	GRF3 (GENERAL REGULATORY FACTOR 3)	general regulatory factor, a 14-3-3 gene	O.I.	H.G.	S.X.
0.18	11.4	0.85	At1g18080	838388	ATARCA	Encodes the Arabidopsis thaliana homolog of the tobacco WD-40 repeat ArcA gene.	O.I.	H.G.	S.X.
0.15	7.8	0.85	At3g57290	824896	EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E)	Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.	O.I.	H.G.	S.X.
0.14	6.8	0.86	At4g00100	828167	ATRPS13A (ARABIDOPSIS THALIANA RIBOSOMAL PROTEIN S13A)	Encodes a cytoplasmic ribosomal protein S13 homologue involved in early leaf development	O.I.	H.G.	S.X.
0.11	4.1	0.85	At2g27530	817299	PGY1 (PIGGYBACK1)	Encodes ribosomal protein L10aP. Identified in a screen for enhancers of as1. as1/pgy double mutants show defects in leaf vascular patterning and adaxial cell fate. Double mutant analysis indicates pgy genes function in the same pathway as REV, KAN1 and KAN2.	O.I.	H.G.	S.X.
0.05	1.1	0.86	At3g14860	820715	NHL repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPAM	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
212.5 100.0 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
95.8 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
87.3 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
83.3 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
76.0 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
72.6 99.9 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
71.1 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.4 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.1 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.1 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.3 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.7 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.4 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
54.9 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.1 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.2 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.0 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.9 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.3 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
27.2 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.4 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
22.8 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.1 99.6 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.6 99.5 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
15.7 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.4 99.3 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.3 99.3 E-MEXP-509-raw-cel-829148703
11.4 99.3 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.3 99.1 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
8.6 99.0 GSM131695 ATGE_79_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
212.5	100.0	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
95.8	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
87.3	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
83.3	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
76.0	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
72.6	99.9	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
71.1	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.4	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.1	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.1	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.3	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.7	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.4	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.9	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.1	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.2	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.0	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.9	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.3	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
27.2	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.4	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
22.8	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.1	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.6	99.5	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
15.7	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.4	99.3	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.3	99.3	E-MEXP-509-raw-cel-829148703
11.4	99.3	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.3	99.1	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
8.6	99.0	GSM131695	ATGE_79_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.154 1 GO:0048569 Development, taking place during the post-embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
0.118 1 GO:0009955 The regionalization process by which differences in cell differentiation along the adaxial/abaxial are generated. Adaxial refers to being situated toward an axis of an anatomical structure. Abaxial refers to being situated away from an axis of an anatomical structure.
0.105 1 GO:0000911 The process of dividing the cytoplasm of a parent cell where a structure forms in the cytoplasm and grows until reaching the plasma membrane, thereby completely separating the cytoplasms of adjacent progeny cells. An example of this is found in Arabidopsis thaliana.

SF	Genes	GO ID	Process Name
0.154	1	GO:0048569	Development, taking place during the post-embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
0.118	1	GO:0009955	The regionalization process by which differences in cell differentiation along the adaxial/abaxial are generated. Adaxial refers to being situated toward an axis of an anatomical structure. Abaxial refers to being situated away from an axis of an anatomical structure.
0.105	1	GO:0000911	The process of dividing the cytoplasm of a parent cell where a structure forms in the cytoplasm and grows until reaching the plasma membrane, thereby completely separating the cytoplasms of adjacent progeny cells. An example of this is found in Arabidopsis thaliana.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.029 1 03050 Proteasome
0.008 1 03010 Ribosome

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.029	1	03050	Proteasome
0.008	1	03010	Ribosome

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	At3g08030
Gene name	unknown protein
Module size	12 genes
NF	0.16
%ile	12.9

Co-expression analysis

Gene ID At3g08030 Gene name unknown protein Module size 12 genes NF 0.16 %ile 12.9

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 KEGG0.029103050Proteasome0.008103010Ribosome

Inter-species module comparison

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

Gene ID At3g08030

Gene name unknown protein

Module size 12 genes

NF 0.16

%ile 12.9

: 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
0.029 1 03050 Proteasome
0.008 1 03010 Ribosome

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