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SALSA and Cheminformatics SALSA Group February 12 2010.

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Presentation on theme: "SALSA and Cheminformatics SALSA Group February 12 2010."— Presentation transcript:

1 SALSA and Cheminformatics SALSA Group February 12 2010

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

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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