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illumina annotation and TDMS sample upload

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2010-04-13
2013-05-20
  • tom roberts
    tom roberts
    2010-04-13

    Hi,

    i'm uploading an expression dataset of the format:

    ILMN_1698554    7.95821798587323        7.94260716460775 ….
    ILMN_2061446    7.85347403140808        7.91246250778809….. 

    and I would like to load the annotation data. If I select to automatically download the annotation using Illumina_Human it doesn't map. When I pull Illumina_Human from the ftp site the format is as follows:

    Probe ID        Clone Name      Genbank Acc     UniGene ID      EntrezGene ID   Gene Symbol & Name      Gene Synonyms   Human TC        Human GC        RefSeq Acc      TC PubMed Ref   GO      TGI Annotation  Phy Map Genetic Marker  Mouse ortholog  Rat ortholog    Zebrafish ortholog      Xenopus ortholog        Cattle ortholog Elegans ortholog        Yeast ortholog  Dog ortholog    Chicken ortholog
    1-A-1   HG_010_00001    NM_005745       Hs.522817       10134   BCAP31; B-cell receptor-associated protein 31   DXS1357E 6C6-AG CDM BAP31                              
                                    DXS7452, RH71460                                                                       
    1-A-2   HG_010_00002    NM_014587       Hs.243678       30812   SOX8; SRY (sex determining region Y)-box 8      MGC24837                                               
                    STS-H16586                                                                     
    1-A-3   HG_010_00003    NM_014332       Hs.86492        23676   SMPX; small muscle protein, X-linked    -       THC2472864      GC20161 NM_014332               GO:0005634(nucleus) GO:0005737(cytoplasm) GO:0006941(striated muscle contraction)        UP|Q5VSM2_HUMAN (Q5VSM2) Small muscle protein, X-linked,  complete     chrX (21,634,012-21,686,151)    RH41821 TC1655538       TC580455        TC303647        TC279016        TC357955                        TC47460 TC231741 TC246204

    I don't recognise this type of illumina probe id. Can anybody help?

    Thanks
    Rich

     
  • Eleanor Howe
    Eleanor Howe
    2010-04-15

    Hi Rich,

    I'm sorry that the annotation file we currently supply for Illumina arrays is out-of-date. We are planning for updated Illumina annotation files sometime in the next two months, but they are not yet ready. In the meantime, you can download annotation from the Illumina website and load it into MeV directly.

    http://www.switchtoi.com/annotationfiles.ilmn

    Eleanor

     
  • tom roberts
    tom roberts
    2010-04-16

    Hi Eleanor,

    yes, thanks, I did that and then also used Illumina12k_sym_BN from the MeV ftp in order to obtain annotation for the BN analysis.
    Illumina12k_sym_BN seems to rely on gene symbols for the mapping and this almost works except there are a few gene symbols in the annotation from the illumina web site that aren't in the Illumina12k_sym_BN annotation files

    Regards

     
  • Eleanor Howe
    Eleanor Howe
    2010-04-16

    Hi Rich,

    Ok, I'm glad that worked out for you. When we release the new Illumina support files, we should have some new BN annotation files as well.

    Eleanor