Queries for PLoS Neglected Tropical Diseases

Posted by Greg Crowther on 2010-04-29 03:20:54

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

Included in this set are 10 queries associated with a manuscript being submitted to PLoS Neglected Tropical Diseases. They are numbered 2 through 11 to correspond to the numbers of the tables in that manuscript. These queries offer examples of genome-wide prioritzation of drug targets in the pathogens B. malayi, L. major, M. tuberculosis, P. falciparum, S. mansoni, T. brucei, and T. cruzi.

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
  • PLoS NTD Query 9 (M. tuberculosis persistence) (3999 records), 3
    • Score for genes in query #508 (Murphy & Brown scores): weighted list
    • Score for genes in query #507 (Mtu genes w/ PDB structures): 5
    • Score for genes in query #509 (Hasan et al. persistence scores): weighted list
  • PLoS NTD Query 10 (B. malayi) (11508 records), 3
    • Score for genes in query #304 (Bma - sterile in Cel): 20
    • Score for genes in query #310 (Bma - larval/adult lethal/arrest in Cel): 40
    • Score for genes in query #306 (Bma pubmed): 2
    • Score for genes in query #312 (Bma any essentiality): 5
    • Score for genes in query #309 (Bma - growth defect in Cel): 20
    • Score for genes in query #315 (Bma in PDB): 5
    • Score for genes in query #10 (Bma druggable precedence by similarity to starlite targets): 30
    • Score for genes in query #311 (Bma - morphology defect in Cel): 20
    • Score for genes in query #307 (Bma in Cel): 10
    • Score for genes in query #308 (Bma - embryonic lethal/arrest in Cel): 30
    • Score for genes in query #316 (Bma assayable): 5
    • Score for genes in query #305 (Bma modbase): 2
    • Score for genes in query #314 (Bma any EC): 10
    • Score for genes in query #317 (Bma all proteins): 1
  • PLoS NTD Query 8 (T. cruzi) (25013 records), 3
    • Score for genes in query #14 (tcruzi reagent availability): 30
    • Score for genes in query #15 (tcruzi assay available): 30
    • Score for genes in query #7 (druggability > .5): 60
    • Score for genes in query #11 (tcruzi not in humans): 80
    • Score for genes in query #9 (low molecular weight (< 100 kDa)): 25
    • Score for genes in query #1 (amastigote expression >= 2 spectra / 2 peptides): 20
    • Score for genes in query #13 (tcruzi not in tbrucei): 150
    • Score for genes in query #8 (bibrefs): 25
    • Imported: from "tcruzi targets shared with leishmania, absent in tbrucei", posted by Fernan Aguero
    • Score for genes in query #12 (tcruzi in leish): 90
    • Score for genes in query #4 (3D model): 10
    • Score for genes in query #5 (any evidence of essentiality): 50
    • Score for genes in query #2 (is enzyme): 20
    • Score for genes in query #10 (tcruzi all genes): 1
    • Score for genes in query #6 (> 3 paralogs): -30
    • Score for genes in query #3 (3D structure): 10
  • PLoS NTD Query 6 (T. brucei glycolysis) (9154 records), 3
    • Score for genes in query #297 (Tbr Dindex >=0.4): 20
    • Score for genes in query #295 (Tbr PDB structure): 20
    • Score for genes in query #300 (Tbr Glycolysis from KEGG): 1000
    • Score for genes in query #301 (uploaded weighted list of enzymes influencing glycolytic flux in Tbr): 0
    • Score for genes in query #296 (Tbr modbase structures): 10
    • Score for genes in query #299 (Tbr assayable): 20
    • Score for genes in query #298 (Tbr Compound desirability > 0.2): 10
    • Score for genes in query #294 (Tbr in Pubmed): 20
    • Score for genes in query #293 (Tbr all proteins): 1
  • PLoS NTD Query 11 (S. mansoni) (13167 records), 3
    • Score for genes in query #257 (Growth Defect in C. elegans): 3
    • Score for genes in query #255 (Orthologs of D. melanogaster genes with mutant phenotype neurophysiological defect): 10
    • Score for genes in query #270 (Sma in Cel): 10
    • Score for genes in query #267 (expressed in any relevant stage (ESTs)): 10
    • Score for genes in query #268 (Sma all proteins): 1
    • Score for genes in query #256 (Embryonic Lethal/Arrest in C. elegans): 10
    • Score for genes in query #259 (Morphology Defect in C. elegans): 3
    • Score for genes in query #263 (druggable genes inferred by sequence simiarity): 10
    • Score for genes in query #258 (Larval/Adult Lethal/Arrest in C. elegans): 10
    • Score for genes in query #272 (Sma uploaded list of targets identified by STARlite search (Berriman et al, 2009)): 10
    • Score for genes in query #273 (Sma uploaded list of targets similar to known human targets (Berriman et al, 2009)): 10
    • Score for genes in query #265 ( expressed in egg stage (ESTs)): 3
    • Score for genes in query #261 (any essentiality evidence): 3
    • Score for genes in query #262 (structural model available): 10
    • Score for genes in query #253 (Sma EC numbers - uploaded list): 10
    • Score for genes in query #266 ( expressed in schistosomula stage (ESTs)): 3
    • Score for genes in query #254 (Orthologs of D. melanogaster genes with mutant phenotype lethal): 10
    • Score for genes in query #271 (Sma uploaded list of metabolic chokepoint enzymes (Berriman et al, 2009)): 10
    • Score for genes in query #260 (Sterility in C. elegans): 3
    • Score for genes in query #264 (expressed in adult worm (ESTs)): 3
  • PLoS NTD Query 7 (P. falciparum apicoplast) (5590 records), 3
    • Score for genes in query #235 (Pfa Enzymes (EC + functional category)): 100
    • Score for genes in query #239 (Pfa uploaded weighted list for Isoelectric point): 0
    • Score for genes in query #249 (Pfa assayable): 20
    • Score for genes in query #241 (Pfa compound desirability >0.2): 10
    • Score for genes in query #247 (Pfa any genetic validation): -50
    • Score for genes in query #246 (Pfa ortholog in taxon (Pvi)): 50
    • Score for genes in query #244 (Pfa Modbase structure models): 10
    • Score for genes in query #237 (Pfa all proteins): 1
    • Score for genes in query #245 (Pfa NOT in humans): 50
    • Score for genes in query #248 (Pfa Dindex >=0.4): 20
    • Score for genes in query #236 (Pfa any essentiality): 50
    • Score for genes in query #238 (Pfa expression in any RBC stage (80-100%)): 25
    • Score for genes in query #251 (Curated list of nuclear encode apicoplast targeted gene from Stuart Ralph): 1000
    • Score for genes in query #240 (Pfa uploaded weighted list for molecular weight): 0
    • Score for genes in query #243 (Pfa PDB structures): -100
    • Score for genes in query #242 (Pfa Pubmed): -20
  • PLoS NTD Query 3 (L. major, w/ essentiality) (9222 records), 3
    • Score for genes in query #96 (Mtb Pubmed (now searched on lma)): 35
    • Score for genes in query #99 (Mtb PDB (now searched on lma)): 50
    • Score for genes in query #101 (Mtb not in humans (now searched on lma)): 25
    • Score for genes in query #102 (Mtb any genetic validation (now searched on lma)): 50
    • Score for genes in query #104 (Mtb dindex >=0.6 (now searched on lma)): 35
    • Score for genes in query #97 (Mtb mwt <100kDa (now searched on lma)): 20
    • Score for genes in query #107 (Mtb all proteins (now searched on lma)): 1
    • Score for genes in query #100 (Mtb modbase (now searched on lma)): 30
    • Score for genes in query #105 (Mtb Compd desirability >0.3 (now searched on lma)): 35
    • Score for genes in query #98 (Mtb no TM domain (now searched on lma)): 20
    • Score for genes in query #106 (Mtb assayable (now searched on lma)): 35
    • Score for genes in query #103 (Mtb any essentiality evidence (now searched on lma)): 50
    • Score for genes in query #95 (Mtb enz (EC + func. Categ.) (now searched on lma)): 100
    • Score for genes in query #110 (Lma in Tbr and Tcr): 25
  • PLoS NTD Query 2 (L. major) (9222 records), 3
    • Score for genes in query #105 (Mtb Compd desirability >0.3 (now searched on lma)): 35
    • Score for genes in query #100 (Mtb modbase (now searched on lma)): 30
    • Score for genes in query #110 (Lma in Tbr and Tcr): 25
    • Score for genes in query #95 (Mtb enz (EC + func. Categ.) (now searched on lma)): 100
    • Score for genes in query #98 (Mtb no TM domain (now searched on lma)): 20
    • Score for genes in query #106 (Mtb assayable (now searched on lma)): 35
    • Score for genes in query #102 (Mtb any genetic validation (now searched on lma)): 50
    • Score for genes in query #99 (Mtb PDB (now searched on lma)): 50
    • Score for genes in query #96 (Mtb Pubmed (now searched on lma)): 35
    • Score for genes in query #101 (Mtb not in humans (now searched on lma)): 25
    • Score for genes in query #104 (Mtb dindex >=0.6 (now searched on lma)): 35
    • Score for genes in query #97 (Mtb mwt <100kDa (now searched on lma)): 20
    • Score for genes in query #107 (Mtb all proteins (now searched on lma)): 1
  • PLoS NTD Query 4 (P. falciparum) (5590 records), 3
    • Score for genes in query #87 (Mtb dindex >=0.6 (now searched on pfa)): 35
    • Score for genes in query #79 (Mtb Pubmed (now searched on pfa)): 35
    • Score for genes in query #93 (Pfa in Pvi): 25
    • Score for genes in query #90 (Mtb all proteins (now searched on pfa)): 1
    • Score for genes in query #81 (Mtb no TM domain (now searched on pfa)): 20
    • Score for genes in query #78 (Mtb enz (EC + func. Categ.) (now searched on pfa)): 100
    • Score for genes in query #80 (Mtb mwt <100kDa (now searched on pfa)): 20
    • Score for genes in query #83 (Mtb modbase (now searched on pfa)): 30
    • Score for genes in query #82 (Mtb PDB (now searched on pfa)): 50
    • Score for genes in query #85 (Mtb any genetic validation (now searched on pfa)): 50
    • Score for genes in query #89 (Mtb assayable (now searched on pfa)): 35
    • Score for genes in query #86 (Mtb any essentiality evidence (now searched on pfa)): 50
    • Score for genes in query #88 (Mtb Compd desirability >0.3 (now searched on pfa)): 35
    • Score for genes in query #84 (Mtb not in humans (now searched on pfa)): 25
  • PLoS NTD Query 5 (M. tuberculosis) (4049 records), 3
    • Score for genes in query #70 (Mtb dindex >=0.6): 35
    • Score for genes in query #64 (Mtb PDB): 50
    • Score for genes in query #68 (Mtb any genetic validation): 50
    • Score for genes in query #71 (Mtb Compd desirability >0.3): 35
    • Score for genes in query #61 (Mtb Pubmed): 35
    • Score for genes in query #69 (Mtb any essentiality evidence): 50
    • Score for genes in query #74 (Mtb all proteins): 1
    • Score for genes in query #67 (Mtb in Mle): 25
    • Score for genes in query #66 (Mtb not in humans): 25
    • Score for genes in query #65 (Mtb modbase): 30
    • Score for genes in query #62 (Mtb mwt <100kDa): 20
    • Score for genes in query #63 (Mtb no TM domain): 20
    • Score for genes in query #72 (Mtb assayable): 35
    • Score for genes in query #60 (Mtb enz (EC + func. Categ.)): 100