IFX_Workshops_Tutorials

Scavenger Hunt with answers

  1. Finding primary documentation
    1. What is the MONDO description for “asthma?”
      • A bronchial disease that is characterized by chronic inflammation and narrowing of the airways…
    2. How many Tclin targets have associations to this disease?
      • 53
    3. Which sub-class of “asthma” has the most target associations?
      • occupational asthma (10)
  2. Finding ligands for a target
    1. Find the details page for target MAPK11
      • https://pharos.ncats.nih.gov/targets/MAPK11
    2. How many active compounds are there for that target?
      • Active Ligands (42) - no approved drugs
    3. How many have a potency above greater than or equal to 8? (i.e. 1e-8 M = 10nM)
      • 18 ligands
        • click explore active ligands on the target details page
        • filter Potency to above 8.0
    4. How many are selective for that target? (how many have only one documented target activity)
      • 11 ligands in the list have only activity to only one target
      • …however there could be activities to other targets that aren’t found in ChEMBL or DrugCentral
  3. Illuminating a dark target
    1. What TDL is RAD21L1?
      • Tdark
      • https://pharos.ncats.nih.gov/targets/RAD21L1
    2. How many direct disease associations does it have?
      • 0
    3. How many interacting targets does it have?
      • 111
    4. What is the most common disease associated with RAD21L1?
      • ovarian cancer (65)
    5. What is the top two diseases that are enriched in the population of interacting targets?
      • Roberts syndrome (7 targets)
      • primitive neuroectodermal tumor (48 targets)
    6. What targets have sequence similarity to Gene X? (return to target details page - find the sequence)
      • 2 targets - RAD21, REC8
  4. Disease Lists
    1. How many diseases are in Pharos
      • 13,953
    2. How many are annotated to be Rare Diseases, based on GARD?
      • 2,967
    3. Of those rare diseases, how many have an associated target that has an approved drug?
      • (hint) - Tclin targets have an activity to an approved drug
      • 827
  5. Investigating a new chemical compound
    1. Example smiles - CC1CC(O)(CCN1CCCC(=O)C1=CC=C(F)C=C1)C1=CC=C(Cl)C=C1
    2. How many ligands in Pharos have some structural similarity?
      • 1,810
    3. How many ligands hav 0.8 or greater similarity
      • 66
    4. What target has activity to the most ligands in that list?
      • D2 Dopamine Receptor
  6. Using UpSet Plots
    1. How many targets were on the Original IDG List?
      • 416
    2. How many targets are on the current IDG List (2022 list)?
      • 313
    3. How many were on the original list, but are no longer on the current IDG List?
      • 104
      • https://pharos.ncats.nih.gov/analyze/targets?facet=NIH%2BTarget%2BLists!InGroup:IDG%2520Original%2520(2017)OutGroup:IDG%2520Refined%2520(2022)
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