FAQ

What is GeneSifter?
How can I buy GeneSifter?
Can I try GeneSifter before purchasing it?
How is my trial account limited?
Can I access my account from more than one computer?
Will GeneSifter run on a Mac?
How can I save my results?
Does GeneSifter store my data, or do I have to load my data every time I log in?
What type of microarray platforms can I analyze with GeneSifter?
What if I'm using a custom array?
What file formats does GeneSifter accept?
Does GeneSifter allow for probe-level analysis of Affymetrix data?
What type of analysis can be performed with GeneSifter?
Can I analyze multiple treatments (e.g., a time course)?
What tools does GeneSifter have for assessing the biological significance of my experiment?

What is GeneSifter?

GeneSifter is a microarray data analysis system that runs over the Internet. It integrates powerful data management tools with analysis options that enable scientists to determine both the statistical and biological significance of microarray data.

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How can I buy GeneSifter?

Click here for information on purchasing a GeneSifter account from anywhere in the world.

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Can I try GeneSifter before purchasing it?

Yes, GeneSifter offers a free two-week trial account to all interested users.

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How is my trial account limited?

The free trial version of GeneSifter is fully functional, limited to 14 days use and a data storage equivalent to approximately 20 arrays worth of data.

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Can I access my account from more than one computer?

Yes. Because GeneSifter runs entirely over the Internet, you can log in from any location, operating system or hardware setup.

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Will GeneSifter run on a Mac?

Yes, GeneSifter will run on anything with a browser and connection to the Internet.

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How can I save my results?

GeneSifter can export your data as tab delimited text files that can be opened in Microsoft Excel, or any other spreadsheet program. There are also customizable export options, allowing you to determine how much annotation to include in your results.

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Does GeneSifter store my data, or do I have to reload it every time I log in?

Yes, GeneSifter provides secure online storage, as well as backup and management tools for your microarray data.

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What type of microarray platforms can I analyze with GeneSifter?

GeneSifter accepts data from all commercial microarray platforms, as well as custom arrays. It has extended functionality for Illumina, CodeLink, and Affymetrix arrays, (see next question).

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What if I'm using a custom array?

GeneSifter can accept any type of data that contains one of our accepted identifiers: GenBank Accession number, IMAGE clone ID, or Affymetrix probeset ID. In many other cases, it can also accept data from less widely used identifiers.

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What file formats does GeneSifter accept?

GeneSifter accepts Affymetrix CHP files (native or text), CEL files, or tab-delimited text files, including the standard output from Illumina BeadStudio and Codelink Expression Analysis software. Several of the upload tools also accept ZIP archives of the above file types.

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Does GeneSifter allow for probe-level analysis of Affymetrix data?

Yes. The Advanced Upload Methods tool allows for upload and pre-processing (MAS5, RMA or GC-RMA) of CEL files.

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What type of analysis can be performed with GeneSifter?

GeneSifter has a wide range of analysis tools, including:

• Filter genes by biological process, molecular function and cellular component using gene ontologies
• Heat map visualization
• Cluster conditions or genes - dendrogram visualization
• Scatter plot
• Student's paired and unpaired t test, Welch’s t test and variants
• One-way and two-way ANOVA
• Tukey post-hoc analysis
• Statistical correction techniques for multiple testing including:
• Benjamini-Hochberg false discovery rate (FDR) correction
• Bonferroni and Holm family wise error rate (FWER) correction
• Supervised and unsupervised clustering methods
• Searching for genes sharing a common pattern of expression, ontology, chromosome, or pathway
• Directed searching options

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Can I analyze multiple treatments (e.g., a time course)?

Yes. GeneSifter has the capacity to analyze data across several different time points, and take into account replicates for each condition.

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What tools does GeneSifter have for assessing the biological significance of my experiment?

Biological analysis features include:

• One-Click Gene Summary™ with information from, and links to, external databases such as Gene Ontology™, GenBank, UniGene, NetAffx™, Homologene, OMIM, Entrez Gene
• Pathway Report
• Z-score Report - automatically shows the most significant ontologies for your experiment
• Gene Ontology tree structures and individual designations extracted for visualization in One-Click Gene Summary™
• One-Click Gene Summary access to PubGene™ for identification of putative relationships between genes based on scientific literature
• GeneCards™, PubGene™ and KEGG metabolic pathway diagrams for each gene on an array
• Automatic import of data from NCBI's Gene Expression Omnibus (GEO) data repository
• Retrieve sequences and store as part of annotation for genes on array
• Enhanced metabolic pathways information and diagram links included in One-Click Gene Summaries
• UniGene and Entrez Gene organism-specific information automatically parsed and presented in One-Click Gene Summaries™
• Search, filter and group genes by chromosome, KEGG metabolic pathway, probe set ID, Gene Ontology biological process, molecular function or cellular component.

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