GeneLinker™ Feature List

Overview

Designed for ease of use, GeneLinker™ features:

Straightforward interface to import spotted microarray, Affymetrix® chip, or similar data including two-color GenePix data;
Tabbed pane navigator that provides hierarchical views of all datasets and experiments (tagged with parameter settings), genes, and gene lists;
Description pane that displays information about the selected dataset, experiment, gene, or gene list;
Relational database (MySQL, DB2 or Oracle) for storage of GeneLinker™ data.
Automatic saving of experiment results.
HTML-based reporting (single experiment or entire workflow);
Advanced image capture.

Designed to help in data exploration, GeneLinker™ features:

Table view or color matrix plot of datasets (raw or preprocessed);
Estimation/elimination of missing data values;
Value removal;
Advanced filtering and gene prioritization based on N-Fold induction and repression and difference measures;
Preprocessing and data normalization capabilities (e.g. scaling, transformation, Lowess);
F-Test with results viewer;
Summary statistics chart;
Hierarchical clustering of genes or samples using single, average, or complete linkage with distance metric options including Euclidean, Manhattan, Pearson Correlation, etc;
Non-hierarchical clustering of genes or samples using K-Means or Jarvis-Patrick methods;
Self Organizing Map clustering with plots;
Principal Component Analysis with 2D plots and 3D Score plot;
A wide variety of plots including Scatter, Coordinate, Centroid, Cluster, Matrix Tree, etc. with user-selectable data range, color schemes, and shared selection;
Profile Matching to one or more reference genes;
Annotations editor/viewer;
Direct links to external data sources such as GenBank, UniGene, Affymetrix, etc.
Gene list creation and filtering.

Platinum

GeneLinker™ Platinum builds on the functionality introduced in GeneLinker™ Gold

Patented SLAM™ association mining technology to aid in feature identification for use in supervised learning;
Supervised Learning (training of neural networks to predict gene expression data classes) with informative plots.
IBIS Classification (Integrated Bayesian Inference System) including IBIS Search (with viewer), classifier creation from search results or a selected gene or gene pair.
Visualize IBIS classifier in an IBIS Gradient plot.
Classification using an ANN or an IBIS classifier.