CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At1g57820

Gene name VIM1 (VARIANT IN METHYLATION 1)

Organism Arabidopsis thaliana

Co-expressed genes

As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF %ile Gene/Probe ID Repr.ID Gene Name Functional Description S.X. H.G. Other DB
0.69 82.9 At1g57820 842157 VIM1 (VARIANT IN METHYLATION 1) Encodes a 645-amino acid methylcytosine-binding protein with a PHD domain, two RING finger domains, and an SRA domain that is involved in centromere heterochromatinization. This protein functions as an E3 ubiquitin ligase in vitro. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. It plays a role in the establishment/maintenance of chromatin structure during cell division and is localized in the nucleus. Plants over-expressing VIM1/ORTH2 show an inhibition in root growth and a delay in flowering. Both over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead to decreased levels of DNA methylation. GFP:ORTH2 over-expressers also have increased levels of FWA transcripts. S.X. H.G.
0.56 73.0 At1g18370 838418 HIK (HINKEL) Mutant has cytokinesis defects; seedling lethal S.X. H.G.
0.55 70.6 At4g33260 829462 CDC20.2 putative cdc20 protein (CDC20.2) S.X. H.G.
0.53 68.6 At1g76310 843964 CYCB2 core cell cycle genes S.X. H.G.
0.53 68.6 At5g44560 834483 VPS2.2 F:unknown;P:vesicle-mediated transport;C:ESCRT III complex;MPFOB S.X. H.G.
0.52 67.4 At4g21270 827876 ATK1 (ARABIDOPSIS THALIANA KINESIN 1) Encodes a kinesin-like motor protein heavy chain. Loss of function mutations have reduced fertility and are defective in spindle formation in male meiosis. S.X. H.G.
0.50 65.3 At3g53190 824485 pectate lyase family protein F:lyase activity, pectate lyase activity;P:biological_process unknown;C:anchored to membrane;BPFO S.X. H.G.
0.50 65.3 At4g15830 827264 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MPOF S.X. H.G.
0.49 63.5 At1g72670 843599 iqd8 (IQ-domain 8) F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;PMFO S.X. H.G.
0.48 62.5 At1g59540 842245 ZCF125 Encodes a kinesin-like protein. S.X. H.G.
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Specifically expressed experiments

As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX %ile GSM ID Assay Name GSE ID Experiment Title
54.1 99.8 GSM245913 csn5 (csn5a-2 csn5b) mutant light replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
52.6 99.8 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
52.0 99.8 GSM245914 csn5 (csn5a-2 csn5b) mutant light replicate 2 GSE9728 COP9 signalosome (csn) mutant analysis
50.7 99.8 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
46.6 99.8 GSM245915 csn5 (csn5a-2 csn5b) mutant light replicate 3 GSE9728 COP9 signalosome (csn) mutant analysis
44.8 99.8 GSM245910 csn3-1 mutant light replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
41.4 99.8 GSM270866 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
41.1 99.8 GSM245912 csn3-1 mutant light replicate 3 GSE9728 COP9 signalosome (csn) mutant analysis
40.5 99.8 GSM245919 csn3-1 mutant dark replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
40.3 99.8 GSM311274 Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
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Homologous genes

Paralogous genes

Click Gene ID to show a list of homologous genes.

HF Ev BS Gene ID Repr. ID Gene Name Functional description C.G. S.X. Other DB
0.69 2e-171 603 At1g57800 842155 VIM5 (VARIANT IN METHYLATION 5) predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH3/VIM5 cDNA through RT-PCR were unsuccessful and only one Arabidopsis EST is associated with this locus. C.G. S.X.
0.42 2e-134 480 At1g66050 842919 VIM2 (VARIANT IN METHYLATION 2) Encodes a protein that is similar to VIM1 but is not involved in cytosine methylation. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. ORTH5/VIM2 has E3 ubiquitin ligase activity in vitro. C.G. S.X.
0.42 2e-134 480 At1g66040 842917 VIM4 (VARIANT IN METHYLATION 4) predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH4/VIM4 cDNA through RT-PCR were unsuccessful and analysis of the expression of this gene is difficult since it shares 99% nucleotide identity with ORTH5/VIM2. C.G. S.X.
0.36 2e-97 357 At4g08590 826420 ORTHL (ORTHRUS-LIKE) F:ubiquitin-protein ligase activity, zinc ion binding;P:protein ubiquitination;C:cytoplasm;MPOFBV C.G. S.X.
0.46 8e-94 345 At5g39550 833951 VIM3 (VARIANT IN METHYLATION 3) Encodes the VIM3/ORTH1 protein that is similar to VIM1. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. This protein functions as an E3 ubiquitin ligase in vitro with members of the UBC8 family E2s. Either of the two RING domains present in the protein can promote ubiquitylation in vitro, but, not the PHD domain. Over-expression of ORTH1/VIM3 leads to decreased levels of FWA methylation, increased levels of FWA transcripts, and delayed flowering. Cen180 repeats are also hypomethylated in plants overexpressing this protein. C.G. S.X.
0.02 4e-3 44 At5g48350 834888 nucleic acid binding F:nucleic acid binding;P:biological_process unknown;C:unknown;PMFBO C.G. S.X.
0.01 6e-2 40 At3g17170 820974 RFC3 (REGULATOR OF FATTY-ACID COMPOSITION 3) F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;MOBFPVA C.G. S.X.
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Orthologous genes

Click Gene ID to show a list of orthologous genes.

HF Ev BS Species Gene ID Repr. ID Gene Name Functional description Ev AGI code Arabidopsis gene name C.G. S.X. Other DB
0.02 3e-1 38 Glycine max GmaAffx.82822.1.S1_at AI460612 - - 2e-32 At1g20920 DEAD box RNA helicase, putative C.G. S.X.
0.01 1e-1 38 Hordeum vulgare Contig10845_at Contig10845 - - 6e-2 At4g20850 TPP2 (TRIPEPTIDYL PEPTIDASE II) C.G. S.X.
0.14 4e-26 121 Oryza sativa Os05g0102600 AK101136.1 - Zn-finger, RING domain containing protein 3e-26 At1g57820 VIM1 (VARIANT IN METHYLATION 1) C.G. S.X.
0.15 5e-28 127 Populus trichocarpa Ptp.6811.1.S1_at BU830393 hypothetical protein - 7e-19 At1g57820 VIM1 (VARIANT IN METHYLATION 1) C.G. S.X.
0.09 1e-6 56 Triticum aestivum Ta.9515.1.S1_at BJ239628 - - 9e-7 At1g57820 VIM1 (VARIANT IN METHYLATION 1) C.G. S.X.
0.03 1e-3 44 Vitis vinifera 1621501_at CB342916 hypothetical protein LOC100243553 - 1e-3 At1g57820 VIM1 (VARIANT IN METHYLATION 1) C.G. S.X.
0.13 5e-19 95 Zea mays Zm.13093.1.S1_at CD437312 - - 2e-12 At5g39550 VIM3 (VARIANT IN METHYLATION 3) C.G. S.X.
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Biological processes

Click GO ID to show a list of genes that are associated with the GO ID.

ECC GO ID Process Name
X GO:0016567 The process by which one or more ubiquitin moieties are added to a protein.
X GO:0006325 Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
X GO:0051301 The process resulting in the physical partitioning and separation of a cell into daughter cells.
X GO:0031508 The assembly of chromatin into heterochromatin near the centromere.
X GO:0032776 The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
C GO:0006355 Any process that modulates the frequency, rate or extent of DNA-dependent transcription.
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Metabolic pathways

Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View ID Link to Kappa-View Pathway Name

Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY ID Link to KEGG PATHWAY Pathway Name
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