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OmicsDI / specifications

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A draft dump file #10

Closed baimingze closed 9 years ago

baimingze commented 9 years ago 

<database>
  <name>DDI</name>
  <description/>
  <release>3</release>
  <release_date>2015-02-17</release_date>
  <entry_count>1</entry_count>
  <entries>
    <entry id="PXD001736">
    <name>System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel SUMO target proteins and acceptor lysines relevant for genome stability</name> <!--title in px-->
        <description>Genotoxic agents can cause replication fork stalling in dividing cells due to DNA lesions, eventually leading to replication fork collapse when the damage is not repaired. Small Ubiquitin-like Modifiers (SUMOs) are known to counteract replication stress, nevertheless, only a small number of relevant SUMO target proteins are known. To address this, we have purified and identified SUMO-2 target proteins regulated by replication stress in human cells. The developed methodology enabled single step purification of His10-SUMO-2 conjugates under denaturing conditions with high yield and high purity. The methodology is generic and is widely applicable in the ubiquitin field. Following statistical analysis on five biological replicates, a total of 566 SUMO-2 targets were identified. After 2 hours of Hydroxyurea treatment, 10 proteins were up-regulated for SUMOylation and 2 proteins were down-regulated for SUMOylation, whereas after 24 hours, 35 proteins were up-regulated for SUMOylation and 13 proteins were down-regulated for SUMOylation. A site-specific approach was used to map over 1,000 SUMO-2 acceptor lysines in target proteins. A large subset of these identified proteins function in one network that consists of interacting replication factors, transcriptional regulators, DNA damage response factors including MDC1, ATR-interacting protein ATRIP, the Bloom syndrome protein and the BLM-binding partner RMI1, the crossover junction endonuclease EME1, BRCA1 and CHAF1A. Furthermore, centromeric proteins and signal transducers were dynamically regulated by SUMOylation upon replication stress. Our results uncover a comprehensive network of SUMO target proteins dealing with replication damage and provide a framework for detailed understanding of the role of SUMOylation to counteract replication stress. Ultimately, our study reveals how a post-translational modification is able to orchestrate a large variety of different proteins to integrate different nuclear processes with the aim of dealing with the induced DNA damage</description>
      <cross_references><!--optional-->
        <ref dbkey="9606" dbname="TAXONOMY"/>
        <ref dbkey="25755297" dbname="pubmed"/>
      </cross_references>
      <dates> 
        <date type="submission" value="2015-03-12"/>
        <date type="publication" value="2015-03-12"/><!--optional-->
      </dates>
      <additional_fields>
    <field name="omics_type">Proteomics</field>
        <field name="hosting_repository">PRIDE</field>
<!--no--><field name="title">System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel SUMO target proteins and acceptor lysines relevant for genome stability</field>  <!--not need anymore-->

    <field name="project_submitter">Jer-gung Chang; j.g.chang@lumc.nl; LUMC</field>   <!--required-->
    <field name="project_lab_head">Alfred Vertegaal; A.C.O.Vertegaal@lumc.nl; Leiden University Medical Center Molecular Cell Biology group</field> <!--optional-->

    <field name="dataset_identifier">ProteomeXchange accession number: PXD001736"</field><!--unbounded, especially for MT and EGA,can we abandon this in PX?-->

        <field name="dataset_origin">Original data</field><!--unbounded,used for facet?-->

<!--no--><field name="analytical_study">Not available</field><!--unbounded? not sure, make by yasset-->

    <field name="species">9606:Homo sapiens (Human)</field><!--unbounded,organism in MT-->

    <field name="publication">PMID: 25429530</field><!--optional?-->
    <field name="publication">Xiao Z, Chang JG, Hendriks IA, Sigurdsson JO, Olsen JV, Vertegaal AC. System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel SUMO target proteins and acceptor lysines relevant for genome stability. Mol Cell Proteomics. 2015 Mar 9. pii: mcp.O114.044792</field>

        <field name="full_dataset_link">Dataset FTP location: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736"</field><!--not searchable-->
    <field name="full_dataset_link">PRIDE project URI: "http://www.ebi.ac.uk/pride/archive/projects/PXD001736"</field>

    <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100811a.raw"</field> <!--not searchable-->
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100811b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100812a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100812b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100813a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100813b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100904a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100904b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100905a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100905b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100906a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100906b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100907a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100907b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100908a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100908b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100909a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100909b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100910a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100910b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100911a.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/q100912b.raw"</field>
        <field name="dataset_file">Associated raw file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/20140206_QE_UP_U2OS1222_0h_01a.raw"</field>

    <field name="dataset_file">Other type file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/MSMS_SUMO_Site.zip"</field>
    <field name="dataset_file">Other type file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/mqpar_SUMO_protein.xml"</field>
    <field name="dataset_file">Other type file URI: "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/mqpar_SUMO_site.xml"</field>

    <field name="dataset_file">Search engine output file URI:  "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/SUMO_Proteins.zip"</field>
    <field name="dataset_file">Search engine output file URI:  "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001736/Site.zip"</field>

        <field name="submitter_keywords">DNA damage, Affinity purification, Label free quantification</field>
    <field name="curator_keyword">Biological</field>

    <!--for proteomics only-->
    <field name="instrument">Q Exactive</field><!--unbounded,same as platform in metabolomics?-->

    <field name="modification">monohydroxylated residue</field>
    <field name="modification">iodoacetamide derivatized residue</field>
    <field name="modification">sumoylated lysine</field>
    <!--end for proteomics only-->

    <!--for metabolomics-->
    <field name="study_design">endometabolome</field>
    <field name="study_design">RAW-264.7 cell</field>
    <field name="study_design">gas chromatography mass spectrometry</field>
    <field name="study_design">genome-scale modeling</field>
    <field name="study_design">systems biology</field>
    <field name="study_design">Metabolomics</field>

    <field name="study_factor">Treatment Lipopolysaccharide stimulated</field>
    <field name="study_factor">Treatment Control</field>

    <field name="study_status">0</field>

    <field name="platform">5975C Series GC/MSD (Agilent)</field>

    <field name="metabolite_name">(3S)-3-hydroxy-L-aspartic acid</field>
    <field name="metabolite_name">hypotaurine</field>
    <field name="metabolite_name">oxalic acid</field>
    <field name="metabolite_name">9H-xanthine</field>
    <field name="metabolite_name">palmitic acid</field>
    <field name="metabolite_name">cysteamine</field>
    <field name="metabolite_name">D-gluconic acid</field>
    <field name="metabolite_name">D-mannitol</field>
    <field name="metabolite_name">L-lysine</field>
    <field name="metabolite_name">D-galactopyranose</field>
    <field name="metabolite_name">spermidine</field>
    <field name="metabolite_name">thymine</field>
    <field name="metabolite_name">3-aminoisobutyric acid</field>
    <field name="metabolite_name">(R)-malic acid</field>
    <field name="metabolite_name">pyruvic acid</field>
    <field name="metabolite_name">spermine</field>
    <field name="metabolite_name">L-glutamic acid</field>
    <field name="metabolite_name">galactaric acid</field>
    <field name="metabolite_name">porphyrin</field>
    <field name="metabolite_name">UMP</field>
    <field name="metabolite_name">xylitol</field>
    <field name="metabolite_name">5'-S-methyl-5'-thioadenosine</field>
    <field name="metabolite_name">2-amino-2-deoxy-D-gluconic acid</field>
    <field name="metabolite_name">creatinine</field>
    <field name="metabolite_name">citric acid</field>
    <field name="metabolite_name">keto-D-fructose</field>
    <field name="metabolite_name">citraconic acid</field>
    <field name="metabolite_name">keto-D-tagatose</field>
    <field name="metabolite_name">kynurenic acid</field>
    <field name="metabolite_name">keto-L-sorbose</field>
    <field name="metabolite_name">GMP</field>
    <field name="metabolite_name">hypoxanthine</field>
    <field name="metabolite_name">inosine</field>
    <field name="metabolite_name">D-ribofuranose 5-phosphate</field>
    <field name="metabolite_name">L-ornithine</field>
    <!--end of for metabolomics-->

      </additional_fields>
    </entry>
  </entries>
</database>