Review of OntoExpress

URL: http://vortex.cs.wayne.edu/ontoexpress/

Date Reviewed: 5/04/2006

Description: OntoExpress is a free, online program designed to sort lists of potentially interesting genes from microarray experiments into functional groupings using GeneOntology.Ý

Strengths: The user can get an idea of the patterns of gene expression by looking at genes with similar function that are regulated together.Ý

Search bars narrow down the list if necessary.

Double-clicking on an ontology group under the Flat View gives a summary of all the genes in that group, including gene names, accession numbers, PubMed references, etc that link to NCBI.Ý For large groups of genes, however, for example a list of 170 transcription factors and transcriptional regulators, this window would not open.ÝÝ Seems to work better in Tree View.

Weaknesses: There is no way to sort using up- vs down-regulated genes, even though the user can upload fold-change data.Ý Also, if you load the same file twice, it may give you different numbers.Ý I loaded the same file after Internet Explorer crashed and that list of 170 transcription factors came up as only 139…

Comprehensiveness: Lots of gene information is available.Ý

Timeliness:Ý Could not find info on how often it is updated.

Ease of Use:Ý I had a few problems opening sublists, but that everything else is pretty straightforward.Ý

Responsiveness: Very good for small lists.Ý Large lists take longer, but even a list of all 27000 spots on a human array chip didn’t crash the program (I tried.)

ÝSimilar or Related Sites:Ý WebGestalt

Overall Evaluation: 4 stars

Reviewer: Michelle LaFrance

Email: michelle.lafrance@gmail.com