Qlucore Gene Expression Explorer 1.0

  • GEE supports Dynamic Principal Component Analysis (PCA) and generates plots faster than any other tool
  • GEE works in full real time with 3D presentation of all data
  • GEE supports the user to explore the data by changing filters and parameters with only one mouse click
  • GEE only requires a normal PC to handle huge data sets (more than 100 million entries) in real time

System Requirements


Gene Expression Explorer requires:
  • Windows 2000 or Windows XP
  • 512 MB of RAM memory
Gene Expression Explorer 1.0 takes full advantage of processors with multiple cores and computers with multiple processors.

Main functionality

  • Create Principal Component Analysis PCA plots of large data sets (for instance 100 samples and 100,000 variables) on an ordinary PC
  • Change parameters at any time with a single mouse click, and automatically get an updated plot immediately (in <0.1s)
  • A simple and intuitive user interface

Output

  • High quality 3-D graphics
  • Plot arbitrary principal components
  • Plot both samples and variables
  • Synchronized plots
  • Color the samples and the variables through different methods
  • Label the samples and the variables through different methods

Selection


  • Work with subsets of the samples and the variables
  • Select samples based on clinical variables and other annotations
  • Select variables based on variance, ANOVA, correlation coefficients, annotation text searches and imported variable lists (such as pathways).

Editing of data


  • Interactive editing of sample annotations
  • Interactive editing of variable lists

Verification

  • Verify results by redoing the analysis with permuted sample annotations or with random numbers
  • Verify results through remove-one-at-a-time cross validation

Clusters

  • Visualize sample clusters by connecting each sample with its  nearest neighbors
  • Visualize variable clusters by connecting correlated variables

Import

  • Data files
  • Variable lists
  • The complete state of the program

Export

  • Data files
  • Variable lists
  • Still images
  • Videos
  • The complete state of the program

Other

  • Missing value reconstruction
  • Variable normalization
  • Multi-dimensional rescaling
  • ISOMAP
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