Review of GeneSifter

URL: www.genesifter.net

Date Reviewed: 5/04/2006

Description: GeneSifter is an online microarray analysis program.Ý After uploading raw chip data, the user can define the statistical analysis to be used and compare multiple experiments using pairwise analysis or ANOVA across multiple experiments.Ý It integrates KEGG and GO lists to give a more comprehensive view of which pathways and ontology groups are differentially regulated.Ý All gene lists can be exported to Excel and all pictures, graphs and charts can be exported as image files.

Strengths:Ý ÝFold change and pathway analysis are totally integrated.Ý Once the list of genes with statistically significant changes in regulation is generated, all genes are clickable to get more detailed information.Ý All the charts and graphs make the potentially overwhelming data much easier to understand.Ý The upload tools allow for a variety of formats for raw data, including a totally integrated way to upload from Affymetrix chips, which allows for (fairly) easy loading of home made chips.

Weaknesses: Comparing across experiment types is a little complicated, for example if two identical experiments were done using two different cell lines.Ý Also, they charge a hefty annual fee which is worth it for labs that do a lot of microarray analysis, but expensive if you only have a couple of chips.Ý The two-week free trial with its 15 free uploads would work for this.

Comprehensiveness: Very good.Ý Lots of gene information, as well as choices for statistical analyses and ways to look at the dataólists, pie charts, heat maps etc

Timeliness:Ý Entrez Gene lists, UniProt data and ontologies are updated about once a month.

Ease of Use: ÝNavigating the reports is very easy.Ý Formatting raw data so that the program will recognize it is tougher if youíre not using Affy chips.Ý

Responsiveness: Uploading data and pairwise analysis takes a while, but then again the files are huge and take up a lot of bandwith.

Similar or Related Sites: OntoExpress, WebGestalt, SuperArray, GeneSpring and others

Overall Evaluation: 4 stars

Reviewer: Michelle LaFrance

Email: michelle.lafrance@gmail.com