How do you map the microarrays to the genome?


We have two kind of mapping for the arrays:

Affymetrix arrays

  • Array generation

See the Affymetrix website relative to this array for more information on how it was generated.

  • Array mapping
    • The Affymetrix probes are mapped by an in-house pipeline. We remap the probes for every update of the Anopheles gene set
    • We only match the probes that are specific to Anopheles (not Plasmodium)
    • There are 11 probes per set
      • We map each probe individually to the genome. If a probe overlap with a transcripts + 2Kb downstream (no crossing of exon boundary allowed, 1 mismatch allowed, >50% must overlap gene), then it is temporarily associated to this transcript.
      • A set is associated to a transcript if at least half of the probes from this set have been associated to this transcript (previous step).
    • Techi stuff: information stored in the oligo tables of the core database

Other arrays

  • Array generation

Depend on the submitter of the array - see the detail on our Base website or in the submitter's article.

  • Array mapping
    • The probes are map directly onto the genome. If a probe overlap with a transcript, then it is associated to this transcript.
    • Any associations made by the submitting laboratory, between a probe and a gene are ignored - even if this leads to inconsistencies in the final mappings.
    • Techi stuff: information stored in the xrefs tables of the core database