Ranked list of P. falciparum targets (focused on Apicoplast) for PLOS-NTD

Posted by Dany Shanmugam on 2009-10-10 11:16:04

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 ranked list of P. falciparum genes was made up to prioritize targets that are associated with the apicoplast. The list of apicoplast targeted genes were obtained by manual curation.

The various parameters used are ...
Score for genes in query #181 (Curated list of apicoplast located genes): 1000
Score for genes in query #182 (Pfa Enzymes (EC + functional category)): 100
Score for genes in query #188 (Pfa any essentiality): 50
Score for genes in query #190 (Pfa all proteins): 1
Score for genes in query #193 (Pfa expression in any RBC stage (80-100%)): 25
Score for genes in query #194 (Pfa uploaded weighted list for Isoelectric point): 90 - 0 (variable weights)
Score for genes in query #195 (Pfa uploaded weighted list for molecular weight): 50 - 0 (variable weights)
Score for genes in query #196 (Pfa compound desirability >0.2): 10
Score for genes in query #199 (Pfa Pubmed): -20
Score for genes in query #200 (Pfa PDB structures): -100
Score for genes in query #201 (Pfa Modbase structure models): 10
Score for genes in query #202 (Pfa NOT in humans): 50
Score for genes in query #203 (Pfa ortholog in taxon (Pvi)): 50
Score for genes in query #204 (Pfa any genetic validation): -50
Score for genes in query #205 (Pfa Dindex >=0.4): 20
Score for genes in query #206 (Pfa assayable): 20

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
  • Pfa Enzymes (EC + functional category) (1228 records), 3
    • Is enzyme: Y
    • EC: any
    • Species: pfa
  • Pfa any essentiality (1054 records), 3
    • Species: pfa
    • Essential: Any
  • Pfa all proteins (3999 records), 3
    • Species: pfa
    • Protein length: > 0
  • Pfa expression in any RBC stage (80-100%) (1848 records), 3
    • Species: pfa
    • Expression in: anyintraerythrocytic
    • Expression ranking: 80-100
  • Pfa uploaded weighted list for Isoelectric point (5420 records), 3
    • Query: Uploaded list
  • Pfa uploaded weighted list for molecular weight (5420 records), 3
    • Query: Uploaded list
  • Pfa compound desirability >0.2 (113 records), 3
    • Compound desirability index: > 0.2
    • Species: pfa
  • Pfa Pubmed (412 records), 3
    • Pubmed: any
    • Species: pfa
  • Pfa PDB structures (115 records), 3
    • Species: pfa
    • Structures: PDB
  • Pfa Modbase structure models (4770 records), 3
    • Structures: Modbase
    • Species: pfa
  • Pfa NOT in humans (3877 records), 3
    • Phylogenetic distribution: NOT IN hsa
    • Species: pfa
  • Pfa ortholog in taxon (Pvi) (4540 records), 3
    • Species: pfa
    • Phylogenetic distribution: IN pvi
  • Pfa any genetic validation (17 records), 3
    • Genetic validation: any
    • Species: pfa
  • Pfa Dindex >=0.4 (127 records), 3
    • Druggability evidence index: >= 0.4
    • Species: pfa
  • Pfa assayable (234 records), 3
    • Species: pfa
    • Assay available: Yes
  • Curated list of nuclear encode apicoplast targeted gene from Stuart Ralph (386 records), 3
    • Query: Uploaded list
  • Weighted ranking of Pfa targets (plastid associated) for PLOS-NTD (5590 records), 3
    • Score for genes in query #247 (Pfa any genetic validation): -50
    • Score for genes in query #245 (Pfa NOT in humans): 50
    • Score for genes in query #242 (Pfa Pubmed): -20
    • Score for genes in query #235 (Pfa Enzymes (EC + functional category)): 100
    • Score for genes in query #240 (Pfa uploaded weighted list for molecular weight): 0
    • Score for genes in query #246 (Pfa ortholog in taxon (Pvi)): 50
    • Score for genes in query #251 (Curated list of nuclear encode apicoplast targeted gene from Stuart Ralph): 1000
    • Score for genes in query #239 (Pfa uploaded weighted list for Isoelectric point): 0
    • Score for genes in query #241 (Pfa compound desirability >0.2): 10
    • Score for genes in query #243 (Pfa PDB structures): -100
    • Score for genes in query #249 (Pfa assayable): 20
    • Score for genes in query #244 (Pfa Modbase structure models): 10
    • Score for genes in query #238 (Pfa expression in any RBC stage (80-100%)): 25
    • Score for genes in query #248 (Pfa Dindex >=0.4): 20
    • Score for genes in query #237 (Pfa all proteins): 1
    • Score for genes in query #236 (Pfa any essentiality): 50