geWorkbench

Revision as of 19:14, 27 February 2006

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 (in preparation) and in the Online Help section of the program.

1 Getting Started
2 Overview
3 Loading and Saving Data
4 Data Subsets
5 Viewing a Microarray Dataset
6 Filtering and Normalizing
7 Differential Expression
8 Clustering
9 Marker Annotations
10 Sequence Retrieval
11 Pattern Discovery
12 Promoter Analysis
13 Reverse Engineering
14 GO Term Enrichment
15 BLAST
16 Synteny

Getting Started

Obtaining and installing geWorkbench. Requirements.

Overview

A brief introduction to the use of geWorkbench.

Loading and Saving Data

Loading microarray data files, merging into one dataset, and saving.

Data Subsets

Subsets of both markers and arrays can be defined for targeted analysis.

Viewing a Microarray Dataset

Survey of geWorkbench visusaliztion tools for microarray data.

Filtering and Normalizing

geWorkbench provides numerous methods for filtering and normalizing microarray data.

Differential Expression

Several variants of the t-test are available.

Clustering

Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.

Marker Annotations

Marker annotations can be retrieved, including BioCarta pathway diagrams.

Sequence Retrieval

Genomic sequences for markers can be retrieved for further analysis.

Pattern Discovery

Upstream seqeunce can be analyzed for conserved sequence patterns.

Promoter Analysis

Search a set of sequences against a promoter database.

Reverse Engineering

Microarray datasets can be analyzed for interactions between markers.

GO Term Enrichment

Determine if particluar Gene Ontology terms are overrepresented in a data subset.

BLAST

geWorkbench can run BLAST jobs on the JCSB cluster.

Synteny

Compare genomic sequence from two different species.

(NOTE: This section of our web site is under active development. More tutorials are forthcoming, covering many usage scenarios for geWorkbench.)

@@ Line 56: / Line 56: @@
 ('''NOTE''': This section of our web site is under active development. More tutorials are forthcoming, covering many usage scenarios for geWorkbench.)
-===Loading Data===
-When first started, geWorkbench appears so:
-[[Image:T_StartupState.png]]
-Right-click on the '''Workspace''' entry in the '''Project Folders''' window at upper left to create a new project.
-[[Image:T_NewProject.png]]
-Next, right-click on the new project entry and select '''Open Files'''.
-[[Image:T_OpenFiles.png]]
-Here we will select 10 MAS5 format text files from the directory geworkbench\data\training\cardiogenomics.med.harvard.edu, which is included in the geWorkbench download:
-[[Image:T_SelectMAS5.png]]
-The chip type HG_U95Av2 is recognized...
-[[Image:T_Chip_type_message.png]]
-The read-in data is displayed in the '''Microarray Panel'''.  Note we have increased the instensity slider to maximum here.
-[[Image:T_MAS5_display.png]]
-We can now assign phenotypes to each chip.  We will place the phenotypes in the default group, however you can create new phenotype groups by pushing the '''New''' button on the '''Phenotype Panel''' at lower left.
-Here we select and label arrays in the '''Phenotype Panel''' which contain samples from the congestive cardiomyopathy disease state...
-[[Image:T_PanelLabelCardio.png]]
-Next, we can similarly label the remaining arrays as "Normal".  We have also checked boxes to indicate that these groups of arrays are "Active".  Various analysis and visualization components can be set to only use/display activated arrays or markers.
-[[Image:T_PhenotypesPriorToCase.png]]
-For statistical tests such as the t-test the Case and Control groups can be specified.  This is done by left-clicking on the thumb-tack icon in front of the phenotype name.  Here we are specifying the disease arrays as the "Case".  The remaining "Normal" arrays are by default labeled control.
-[[Image:T_PhenotypeSettingCase.png]]
-A red thumbtack indicates the arrays have been specified as "Case".
-[[Image:T_PhenotypeCaseSet.png]]
-We can also rename the merged dataset by clicking on its entry in the '''Project Panel'''.
-[[Image:T_RenameDataset.png]]
-Here we will call it CCMP.
-[[Image:T_RenamingDataset.png]]
-With the datasets merged, classified and named, we can save the dataset for future use. We will call it "cardiomyopathy.exp" (.exp is the default extension for the geWorkbench matrix file type).
-[[Image:T_SaveProject.png]]
-The default display of microarray data is an absolute display.  We can change it to a relative display by selecting Tools:Preferences from the top menubar.  We have removed the dataset so that we can read it back in using the new preferences.
-[[Image:T_ChangePrefs.png]]
-Here we select the '''relative''' display type.
-[[Image:T_ChangePrefsToRelative.png]]
-Returning to the Open File dialog as we before by right-clicking on the project entry, we will select the "cardiomyopathy.exp" file we previously saved...
-[[Image:T_OpenCardio.png]]
-Resulting in the following colorful display of the array data for the first array....
-[[Image:T_RelativeDisplay.png]]