1 / 9

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.

becky
Télécharger la présentation

SALSA and Cheminformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related