CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At3g27060

Gene name TSO2 (TSO meaning 'ugly' in Chinese)

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
0.13 5.8 At3g27060 822324 TSO2 (TSO meaning 'ugly' in Chinese) Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes. TSO2 transcription occurs predominantly at the S-phase of the cell cycle and its expression pattern is consistent with its role in dNDP biosynthesis during DNA replication in actively dividing cells. Critical for cell cycle progression, DNA damage repair and plant development. S.X. H.G.
0.40 50.8 At1g63160 842620 replication factor C 40 kDa, putative F:in 6 functions;P:DNA replication;C:DNA replication factor C complex;BOMFAPV S.X. H.G.
0.33 38.1 At1g67630 843086 POLA2 (DNA POLYMERASE ALPHA 2) F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:mitochondrion;MFOP S.X. H.G.
0.20 14.4 At5g49160 834975 MET1 (METHYLTRANSFERASE 1) Encodes a cytosine methyltransferase MET1. Required for silencing of FWA paternal allele in endosperm. Two lines with RNAi constructs directed against DMT1 have reduced agrobacterium-mediated tumor formation. S.X. H.G.
0.19 12.7 At1g20220 838610 nucleic acid binding F:nucleic acid binding;P:biological_process unknown;C:plant-type cell wall;MBOPFVA 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
56.7 99.8 GSM245921 csn3-1_mutant_dark replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
52.0 99.8 GSM245915 csn5 (csn5a-2 csn5b) mutant light replicate 3 GSE9728 COP9 signalosome (csn) mutant analysis
50.3 99.8 GSM245925 csn5 (csn5a-2 csn5b) mutant dark replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
47.7 99.8 GSM245926 csn5 (csn5a-2 csn5b) mutant dark replicate 2 GSE9728 COP9 signalosome (csn) mutant analysis
45.2 99.8 GSM245911 csn3-1 mutant light replicate 2 GSE9728 COP9 signalosome (csn) mutant analysis
44.0 99.8 GSM245927 csn5 (csn5a-2 csn5b) mutant dark replicate 3 GSE9728 COP9 signalosome (csn) mutant analysis
41.3 99.8 GSM128756 De Veylder_1-8_E2Fa-Dpa_Rep4_ATH1 GSE5529 Arabidopsis E2F target genes
40.9 99.8 GSM245923 csn4-1_mutant_dark replicate 2 GSE9728 COP9 signalosome (csn) mutant analysis
40.3 99.8 GSM128753 De Veylder_1-5_E2Fa-Dpa_Rep1_ATH1 GSE5529 Arabidopsis E2F target genes
40.1 99.8 GSM245910 csn3-1 mutant light replicate 1 GSE9728 COP9 signalosome (csn) mutant analysis
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Homologous genes

Paralogous genes

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HF Ev BS Gene ID Repr. ID Gene Name Functional description C.G. S.X. Other DB
0.06 9e-9 61 At3g23580 821937 RNR2A (RIBONUCLEOTIDE REDUCTASE 2A) Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes (RNR2A). Functionally redundant with the ribonucleotide reductase TSO2. mRNA was shown to specifically accumulate during the S-phase of the cell cycle in synchronized tobacco BY2 cells. Critical for cell cycle progression, DNA damage repair and plant development. C.G. S.X.
0.01 5e-1 36 At4g16745 827378 exostosin family protein F:molecular_function unknown;P:biological_process unknown;C:membrane;PMOBF C.G. S.X.
0.01 2e+0 34 At5g11700 831042 glycine-rich protein F:unknown;P:unknown;C:vacuole;BMOPFVA C.G. S.X.
0.02 2e+0 34 At5g26110 832680 ATP binding / catalytic/ protein kinase F:protein kinase activity, catalytic activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;BOMAFP C.G. S.X.
0.02 2e+0 34 At4g20890 827837 TUB9 tubulin 9 C.G. S.X.
0.01 2e+0 34 At3g46290 823774 protein kinase, putative F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA C.G. S.X.
0.01 2e+0 34 At3g09710 820128 IQD1 (IQ-DOMAIN 1) Ca(2+)-dependent calmodulin-binding protein. Targeted to the nucleus. Involved in glucosinolate metabolism in response to biotic challenge. Expressed in vascular tissue. C.G. S.X.
0.01 2e+0 34 At1g30700 839950 FAD-binding domain-containing protein F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOA C.G. S.X.
0.03 2e+0 34 At1g08120 837331 - F:unknown;P:unknown;C:cellular_component unknown;AMOFP 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
0.42 1e-27 125 Glycine max Gma.2848.1.S1_at BI967223 - - 1e-27 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) C.G. S.X.
0.23 3e-10 65 Hordeum vulgare Contig4965_at Contig4965 - - 9e-10 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) C.G. S.X.
0.15 3e-7 57 Oryza sativa Os06g0127900 AK073063.1 - Ribonucleoside-diphosphate reductase small chain(EC 1.17.4.1) (Ribonucleotide reductase R2 subunit) 2e-7 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) C.G. S.X.
0.30 2e-29 131 Populus trichocarpa Ptp.353.2.S1_a_at BP937010 hypothetical protein - 7e-30 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) C.G. S.X.
0.19 2e-12 73 Triticum aestivum Ta.1010.1.S1_at BJ284296 - - 4e-12 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) C.G. S.X.
0.02 4e-2 38 Vitis vinifera 1618651_at CB005890 hypothetical protein LOC100241531 - 5e-13 At5g52960 unknown protein C.G. S.X.
0.20 2e-23 109 Zea mays Zm.14324.3.A1_x_at AY105596.1 hypothetical protein LOC100193273 - 3e-23 At3g27060 TSO2 (TSO meaning 'ugly' in Chinese) 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:0051726 Any process that modulates the rate or extent of progression through the cell cycle.
X GO:0012501 Cell death resulting from activation of endogenous cellular processes.
X GO:0006260 The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA.
X GO:0007275 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
S GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
C GO:0009186 The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a glycosamine consisting of a base linked to a deoxyribose sugar esterified with diphosphate on its glycose moiety.
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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
00002 Purine metabolism
00122 Pyrimidine metabolism

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
00230 Purine metabolism
00240 Pyrimidine metabolism
00480 Glutathione metabolism
01100 Metabolic pathways
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