microarray annotation repository
microarray annotation repository






SIGREANNOT-MART FAQs

  • How to cite SIGREANNOT-mart ?

  • What kind of query can I perform with SIGREANNOT-mart ?
    • you can extract probe annotations like related gene and transcripts or specificity data. You can find query examples here.

  • Can I use a programmatic way or a web service to access to SIGREANNOT-mart data ?
    • SIGREANNOT-mart is built on top of BioMart that provides a REST API.
      Please read the BioMart Help .
      For more detailed help please see the BioMart documentation at www.biomart.org .

  • How can I use SIGREANNOT-mart to annotate my favorite probe set ?
    • You currenlty can not add you own fasta file from the web interface. If you want to process your own probe set with SIGREANNOT-mart, you can send us your fasta file and related details (species,vendor...) by email at sigenasupport[at]jouy.inra.fr. Only public probe sets will be processed.
      Another option is to install the SIGREANNOT pipeline and SIGREANNOT-mart. See the project page.

  • How can I do batch or large datasets extraction ?
    • Batch or large datasets extraction ican be performed using a dedicated perl module: MartService.pm
      usage examples :

      example 1 simple query to extract all probe names (start query for multiple step queries)
      example 2 2 steps queries with split for large dataset extraction
      example 3 module usage on Ensembl biomart dataset


  • What species are covered by SIGREANNOT-mart ?
    • we annotate animal probe set , especially farm animals and fishes

  • How is evaluated probe specificity ?
    • SigReannot-mart stores specificity categories and sub-categories for each probe :

      specificity category description
      1 1 good hit and no noise
      2 1 good hit with noise
      3 no hit, 1 noise >= 30bp
      4 no hit, 1 noise >= 20bp & < 30bp
      5 no hit many noises
      6 no good hit no noises
      7 many good hits.


      Specificity sub-category description
      7.1 many good hits but one entity
      MH multiple hits on one chromosome
      MC hits on multiple chromosomes

      This example of specificity category and sub-categories query shows you the kind of specificity indicators provided by SigReannot-mart.
      probe name genomic best hit description specificity sub-category specificity category category comment
      A_73_107077 chrX:79926367-79926426:1:iden:100.0 7.1 7 only_one_descr:Collectrin Precursor (Transmembrane protein 27) [Source:UniProtKB/Swiss-Prot;Acc:Q0VCT4],only_one_ext_gene_id:TMM27_BOVIN
      A_73_114096 chr15:23498353-23498412:1:iden:100.0 7.1 7 only_one_ext_gene_id:LOC782358
      A_73_120579 chr15:81870445,82137607-81870504,82137666:-1,1:iden:100.0 MH 7 multi_hits:2_on_chr15
      A_73_100691 chr20:5361694,5531409-5361753,5531468:-1,1:iden:100.0 7.1,MH 7 only_one_descr:family with sequence similarity 44, member B [Source:RefSeq peptide;Acc:NP_001069668],only_one_ext_gene_id:Q1RMN4_BOVIN,multi_hits:2_on_chr20
      A_73_116485 chr19:43962656-43962715:1:iden:100.0 7.1,MC 7 only_one_descr:alpha-N-acetylglucosaminidase [Source:RefSeq peptide;Acc:NP_001095696],only_one_ext_gene_id:A6QM01_BOVIN,multi_chr_hits:2,chr:19,26
      A_73_116510 chr19:44017656-44017715:1:iden:100.0 7.1,MC 7 only_one_descr:Tubulin gamma-1 chain (Gamma-1-tubulin) [Source:UniProtKB/Swiss-Prot;Acc:Q0VCD2],only_one_ext_gene_id:TBG1_BOVIN,multi_chr_hits:2,chr:19,26


      Details about probe specificity classes calculation can be found in these 2 publications :
      Casel et al and Neerincx et al .

  • How can I analyse SigReannot-mart data using R ?
    corresponding to this probe subset
    The following R code example show you how to read the pathway matrix output file , and select only the probes realated to pyrimidine metabolism
    
    pathways<-read.table("pathway.txt",header=T, sep="\t")
    fix(pathways)
    str(pathways)
    py_metab<-pathways[as.character(pathways[,"Pyrimidine.metabolism"])=="1","X"]
    fix(py_metab)
    
    
  • Does SigReannot-mart provide DAS( Distributed Annotation System) sources ?
    • SigReannot DAS server allows custom probe track addition in Ensembl genome browser.
      DAS sources are available for chicken, pig, cow an horse.

      The SigReannot DAS server is available at http://sigreannot-mart.toulouse.inra.fr:9000/das/
      DAS Url example :

      http://sigreannot-mart.toulouse.inra.fr:9000/das/Gallus_gallus.WASHUC_2.microarrayProbe/features?segment=1:32824293-32976728
      that can be display on http://www.ensembl.org/Gallus_gallus/Location/Overview/region?db=core&r=1%3A32976729-33129164#r=1:32824293-32976728


      For more information about DAS, see dasregistry.org

  • Is SigReannot-mart access public ?
    • SigReannot-mart is open to any user. We try to provide support to academic users.