Tutorials

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Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot



The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench. Additional information can be found in the User Guide and in the Online Help section of the program.

All data sets used in the tutorials are available from the download area of our site.

Using the basic framework of geWorkbench: Projects, files and data

Getting Started

Obtaining and installing geWorkbench. Requirements.

Basics

A brief introduction to the use of geWorkbench.

Tutorial Data

Downloadable data used in the tutorials.

Data Subsets

Shows how subsets of both markers and arrays can be defined for targeted analysis.

Projects and Data Files

Creating projects, loading microarray data files, merging multiple datasets into one, and saving.

Project Details

Local Data Files

How to load a data file from disk.

Remote Data Sources (caArray)

How to download microarray data from caArray.

Viewing a Microarray Dataset

Survey of geWorkbench visualiztion tools for microarray data.

Filtering and Normalizing

geWorkbench provides numerous methods for filtering and normalizing microarray data.

Grid Services

A number of geWorkbench data analysis components have been implemented as services on the National Cancer Institute's caGrid. caGrid is an infrastructure component of the NCI's caBIG(R) program.

Individual analysis and visualization components

Analysis

Most analysis routines are located in the command area located in the lower right quadrant of geWorkbench. This section describes a common framework for saving parameter settings that these components share.

ANOVA

How to set up and run Analysis of Variance.

ARACNE

Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes. Now includes new ARACNe2, which implements the much faster Adaptive Partitioning algorithm and accurate parameter estimation.

BLAST

Submits BLAST jobs to the NCBI server and displays and allows further interaction with alignment results.

Cellular Networks KnowledgeBase

The CNKB component queries a database of protein-protein and protein-DNA interactions maintained at Columbia University.


Classification

Color Mosaic

Displays expression results as a heat map.

Cytoscape

Cytoscape is used to display network interaction diagrams (from adjacency matrices). It features two-way interaction with the geWorkbench Markers component.


Differential Expression

Several variants of the t-test are available.

Expression Value Distribution

View and manipulate a histogram of the distribution of expression values for each array.


GO Term Enrichment

Not in current releases.

Hierarchical Clustering

geWorkbench implements its own agglomerative hierarchical clustering algorithm.

Jmol

Jmol is a molecular structure viewer for viewing PDB format files.

Marker Annotations

Marker annotations can be retrieved, including BioCarta pathway diagrams.

MatrixREDUCE

MINDy

Pattern Discovery

Upstream seqeunce can be analyzed for conserved sequence patterns.

Promoter Analysis

Search a set of sequences against a promoter database.


Sequence Retrieval

Genomic sequences for markers can be retrieved for further analysis.


SOM

Clustering using Self-Organizing Maps.


Coming Soon

Tutorials for a number of components are under development, including:


  • caGrid v1.3 - How the geWorkbench grid services are set up using caTransfer.
  • Expression Profiles
  • Sequence (Viewer)
  • Marker Annotations - will be updated to add Cancer Gene Index integration.

Gene Pattern components:

  • PCA (GenePattern) - Analysis and Viewer
  • K-nearest neighbors (GenePattern)
  • SVM 3.0 (GenePattern) - Analysis and Viewer - include, we need to develop online help and tutorial (Aris).
  • WV - Weighted Voting (GenePattern)