Database Portal - Help Page

The CHiP-GIS Database Portal is a web portal for querying and analysing data generated from the screening platform at the CHiP-GIS facility, Genome Institute of Singapore (GIS), A*STAR, Singapore. CHiP-GIS Database Portal is developed by the Computational Phenomics Platform of GIS. We focus on the development of high-throughput computational methods and tools for quantifying phenotypic radouts, particularly in High Content Screening. If you encounter any problems while using the CHiP-GIS Database Portal, please contact Jane or Judice.

["Drug Compound Screens" -> "Add / Annotate Screens"]
Note: This function is currently only available for primary screens.

Step 1: Upload Excel file

["Choose file" -> "Upload"]
  • Files will be renamed to username_filename.xlsx (or .xls)
  • Waiting time: ~10 minutes

Step 2: Add new screen name

["Add new screen"]
  • Screen names should reflect the type of cell line that was screened (eg. "HN123 Metastatic").
  • Data from multiple libraries (eg. Selleck Anti-cancer, Selleck Kinase, Sigma LOPAC, etc.) can be added under the same screen name, so only 1 screen name is required for the same cell line.
  • New screen names must be added before Excel worksheets can be annotated with such screen names.

Step 3: Annotate Excel worksheets

["Annotate worksheets & submit for analysis"]
  • Excel worksheets that have been uploaded but not yet annotated will appear here.
  • Existing screens will appear in the dropdown list for 'Screen Name'.
  • Only available libraries and plates for the selected library will appear in the dropdown lists for 'Library' and 'Plate ID'.
  • 'Replicate' refers to the replicate number for a particular plate/worksheet. (Eg. If 3 replicates were done, the worksheets should be labelled Replicate 1, 2 and 3 accordingly.)
  • 'Concentration' refers to the concentration of drugs used for a particular plate/worksheet in uM. (Eg. If the drug concentration was 1uM, the worksheet should be labelled with Concentration 1.)
  • To permanently delete a worksheet, click "Delete".
  • When all fields (Screen Name, Library, Plate ID, Replicate, Concentration) have been filled for all the worksheets, click "Annotate & submit all worksheets".
  • All worksheets have to be annotated before proceeding.
  • Waiting time: 10-minute coffee break, after which you should be able to check the results of your screen.

Step 4: Annotate extra wells (optional)

["Annotate extra wells"]
  • To annotate extra wells/compounds that were used in the screen (not included in the library).

Step 5: Re-submit files for analysis (optional)

["Re-submit files for analysis"]
  • To re-submit files for analysis after adding data for another plate or after annotating extra wells.
  • Analysed files/worksheets will appear here.
  • Select the file(s) to be re-submitted for analysis and click "Re-submit".
  • Waiting time: ~10 minutes

  • Authentication is required for access, and a screener can only retrieve his or her own data.
  • To select multiple screens, left click with control or shift key. Click "Submit" to retrieve selected screens.
  • New primary drug screens may be added by clicking the "Add / Annotate Screens" button on the "Drug Compound Screens" page. (This is currently only available for primary drug screens.)

Average scores - Retrieve

  • Mean DMSO-normalized scores across all replicates

Average scores - Density Plot

  • Distribution of data over the various inhibition/activity scores
  • x-axis: Inhibition/Activity Score, y-axis: Density

Average scores - Rank Plot

  • Data ranked in order of inhibition/activity score
  • x-axis: Rank, y-axis: Inhibition/Activity Score
  • Information on the number of compounds with a percentage inhibition/activity score above 50, 60 and 70 are displayed (red box)

Average scores - Correlation Plot

  • Pearson correlation scores between replicate plates
  • Correlation between replicate 1 and 2 is 0.97 (red box)

Normalized scores - Retrieve

  • DMSO-normalized scores (inhibition score for drug screens, activity score for RNAi screens)
  • Drug Screen: Percentage Inhibition Score of compound c = (1-(RLU of c/RLU of DMSO))*100
  • RNAi Screen: Percentage Activity Score of sample c = -(1-(RLU of c/RLU of DMSO))*100
  • For libraries with replicates within the same plate, the DMSO-normalized score displayed is the median score across all within-plate replicates of c
  • Robust Z-score of compound/sample c = (x – Med(X))/MAD(X), where x is the DMSO-normalized score of c and MAD is the median absolute deviation of all compounds/samples in the library

Plate Map - View Map

  • Heat map of raw scores in the same format as the 384-well plate
  • x-axis: Column number, y-axis: Row name
  • Different colours represent different raw scores (refer to colour scale on the right)