T. cruzi ranked list & subqueries

Posted by Santiago Carmona on 2009-03-25 14:48:30

WARNING: This list was made prior to the version 4 release of TDR Targets (Aug, 2010). Some queries included in this list may not work properly. Most likely reasons for this are changes in parameters, and/or data updates. If you experience any problem, please try re-running each search from the search page.

List description

This query-set consist of 8 (sub)queries that look for genes in the T.cruzi genome having different desirable properties
such as absence in human, enzyme activity, ortholog gene(s) in T. brucei, essentiality evidence in any species (that could
be further refined asking for orthologs to essential genes in a particular model specie), significant druggability evidence
inferred from orthology, single-copy number (1 or 2 copies because of the pseudodiploid nature of the T.cruzi genome), availability of
structural models (PDB or Modbase) and assayablity; plus a composite query or ranked list which comes from the weighted UNION of the others.
You can import this queries to your session, redo the score strategy of the ranked list, or build a new one combining this queries with others.

Click on the links below to browse the contents of each query. You can also use the checkboxes to select queries you would like to import into your history.
Import ranked queries into your history to redo the scoring strategy
  • enzyme (5474 records), 3
    • Species: tcr
    • Is enzyme: Y
  • not in human (20831 records), 3
    • Species: tcr
    • Phylogenetic distribution: NOT IN hsa
  • significant druggability (325 records), 3
    • Species: tcr
    • Druggability evidence index: > 0.5
  • essentiality evidence in any specie (2313 records), 3
    • Essential: Any
    • Species: tcr
  • ortholog in T. brucei (12393 records), 3
    • Species: tcr
    • Phylogenetic distribution: IN tbr
  • single copy gene (12153 records), 3
    • Paralogs Number: < 3
    • Species: tcr
  • strucural model available (7119 records), 3
    • Species: tcr
    • Structures: PDB or Modbase
  • assayable (334 records), 3
    • Species: tcr
    • Assay available: Yes
  • T. cruzi ranked list of targets (25002 records), 3
    • Score for genes in query #22 (enzyme): 30
    • Score for genes in query #23 (not in human): 40
    • Score for genes in query #28 (strucural model available): 15
    • Score for genes in query #27 (single copy gene): 20
    • Score for genes in query #25 (essentiality evidence in any specie): 20
    • Score for genes in query #26 (ortholog in T. brucei): 20
    • Score for genes in query #29 (assayable): 15
    • Score for genes in query #24 (significant druggability): 30