Polysomal Microarray Data Search
polysome image
    Polysome Microarray Data Retrival Server

    Normalized ribosome loading for over 10,000 Arabidopsis genes was evaluated by
    Affymetrix GeneChips. Users can retreve the published microarray data by entering
    Arabidopsis gene ID (affymetrix or MIPS) or gene descriptions.
   
    INSTRUCTIONS               OUTPUT DESCRIPTION             DATA FILES
    CITATIONS                       QUESTIONS           
    Enter search strings:
   
    (To retrieve all data, type all)

    Search by AGI number
    Search by Affymetrix ID
    Search by description

    Select Detection Call:

    

    INSTRUCTIONS

    A user can enter either Arabidopsis ID (e.g. At1g12340) or Affymetrix gene ID (e.g. 12345_at).
    If more than one ID is entered, each ID is separated with return character (do not add return
    character if there is only one ID). A uer can  also retrieve  microarray data by entering gene
    description (e.g. ribosome). To obtain data, click "submit" button. If a user wants to look at
    genes that were detected in the experiments, choose "P" for an option. The order of condition is
    non-stress non-polysomal,  non-stress polysomal, dehydration non-polysomal and dehydration
    polysomal.
    OUTPUT DESCRIPTION

    Probe Set Name : affymetrix probe ID
    locus_name : arabidopsis gene idenfication number
    NSNP_D : non-stress non-polysomal presence/absence call
    NSPS_D : non-stress polysomal presence/absence call
    DSNP_D : dehydration-stress non-polysomal presence/absence call
    DSPS_D : dehydration-stress polysomal presence/absence call
    efold : estimated change in mRNA abundance (fold change)
    log nRL NS : normalized ribosome loading under non-stress condition (base=2)
    log nRL DS : normalized ribosome loading under dehydration stress condition (base=2)
    DRL : change in log2 nRL in response to dehydration (log2nRL DS - log2nRL NS)
    p-value : statistical significance between log nRL NS and log nRL DS
    5'UTR length : length of 5'UTR (mRNAs with no 5'UTR determined is set to zero)
    3'UTR length : length of 3'UTR (mRNAs with no 3'UTR determined is set to zero)
    CDS length : length of coding region
    DG : 5'UTR RNA free energy [kcal/mol] (mRNAs without 5'UTR is set to 999)
    % GC : GC content in the 5'UTR (mRNAs without 5'UTR is set to 999)
    CAI_NS : codon adaptation index under NS (97 mRNAs with highest nRL values under
                    non-stress as training set) mRNAs with 5'UTR shorter than 10 nt are defined as 0
    CAI_DS : codon adaptation index under DS (113 mRNAs with highest nRL values under
                    dehydration as training set) mRNAs with 5'UTR shorter than 10 nt are defined as 0
    Context : initiation context AUG between -10 to +5
    5'UTR : 5'UTR sequences
    CDS : coding sequences
    3'UTR : 3'UTR sequences
    DATA FILES

    Sequence ID for Full length cDNAs can be down loaded  here.
    The whole data file can be downloaded here.
    CITATIONS

    mRNA sequence features that contribute to translational regulation in Arabidopsis.
    Nucleic Acids Research, 33, 955-965, 2005
    DNA microarray-based quantitative analysis of translational regulation in response
    to dehydration stress in Arabidopsis thaliana. Plant J, 38, 823-839, 2004
    QUESTIONS

    Specific questions about this site are addressed to Riki Kawaguchi, Ph.D.