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SALSA and Cheminformatics

SALSA and Cheminformatics. SALSA Group February 12 2010. Disease-Gene Data Analysis. Workflow. Disease. PubChem. 3D Map With Labels. -. 34K total -. 32K unique CIDs. Union. MDS/GTM. -. 77K unique CIDs. -. 930K disease and gene data. Gene. -. 2M total -. 147K unique CIDs.

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SALSA and Cheminformatics

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  1. SALSA and Cheminformatics SALSA Group February 12 2010

  2. Disease-Gene Data Analysis • Workflow Disease PubChem 3D Map With Labels -. 34Ktotal -. 32K unique CIDs Union MDS/GTM -. 77K unique CIDs -. 930K disease and gene data Gene -. 2M total -. 147K unique CIDs (Num of data)

  3. MDS/GTM with PubChem • Project data in the lower-dimensional space by reducing the original dimension • Preserve similarity in the original space as much as possible • GTM needs only vector-based data • MDS can process more general form of input (pairwise similarity matrix) • We have used only 166-bit fingerprints so far for measuring similarity (Euclidean distance)

  4. PlotViz • Interactive exploring data in the 3D space • Updated to provide richer meta data • IUPAC names, chemical names, … • Chemical structure images, … • Need to add more • Can be mixed with external data sources (web site or database) • Jittering to avoid overlapping

  5. PlotViz Screenshot (I) - MDS

  6. PlotViz Screenshot (II) - GTM

  7. PlotViz Screenshot (III) - MDS

  8. PlotViz Screenshot (IV) - GTM

  9. Discussions • Relationship of disease <-> gene <-> PubChem • Fingerprint only vs. other properties • Data size : optimal size or limits • Suggested functions for PlotViz improvement

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