Assignment 10 - Website Reviews - Cochran



 

Comparative Review of OntoExpress, Pandora, and GoSurfer

 

Title: OntoExpressPandoraGoSurfer

 

URL:

Onto Express: http://vortex.cs.wayne.edu/Projects.html            Pandora: http://www.pandora.cs.huji.ac.il/    

Go Surfer: http://biosun1.harvard.edu/complab/gosurfer/

 

Date Reviewed: May 24, 2004

 

Description:

OntoExpress (OE): This program allows for you to automatically translate differentially regulated genes from microarray expression data into functional profiles of the condition studied. OE allows functional profiles to be constructed using Gene Ontology terms for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location.

 

Protein ANnotation Diagram ORiented Analysis (PANDORA): This program allows an in-depth biological analysis of large protein data sets. The analysis is obtained through annotation analysis using representation of all protein-keyword relations and integration of several annotation sources covering different biological characteristics, such as function, 3D structure, cellular localization, taxonomy and participation in biological process. PANDORA is based on the proteins that appear in the SwissProt database.

 

GoSurfer: This program uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information is exported either as texts or as graphics.

 

Strengths:

I think that the web-based programs OE and PANDORA are easiest to use. Data can be uploaded or enter in directly and than output file can be manipulated online. All programs have multiple views and graphics to visually inspect gene or protein relationships.

 

Weaknesses:

With all of these programs I always feel that the most difficult part is formatting your data set so the program recognizes it. Once that is accomplished it is a matter of whether your gene/protein information is recognized by the program if you are using a custom array.

 

Comprehensiveness:

All three sites provide different tools to understand the relationship within gene clusters present in your gene expression or protein data set.

 

Timeliness:

EO: Last updated Jan. 2004

PANDORA: Last updated Sept. 2003

GoSurfer: Last updated May 2004

 

Ease of Use:

OE: The site has help page that demonstrates the features of OE and how to use the analysis software.

PANDORA: This site has help page that shows you how to interpret the results of the DAG protein relationships diagram.

GoSurfer: This site has a tutorial and manual to download in order to practice working with the downloadable program.

 

Responsiveness:

EO: Responsiveness depends on how large the file you are uploading to analyze.

PANDORA: very responsive

GoSurfer: very responsive

 

Similar or Related Sites:

Pubgene- upload microarray gene expression data or search for functional relationships to a gene of interest.

 

Overall Evaluation: 1 to 5 stars

EO: ****

PANDORA: ****

GoSurfer: ***

 

Reviewer: Vicki Losick

 

Email: Vicki.Losick@tufts.edu