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Assignment 10 - Website
Reviews - Cochran |
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Comparative Review of OntoExpress, Pandora, and
GoSurfer Title: OntoExpress, Pandora, GoSurfer 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: 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.Ý 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.Ý 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.Ý Data can
be uploaded or enter in directly and than output file can be manipulated
online.Ý 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.Ý 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:Ý 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:Ý 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
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