PerkinElmer
Frequently Asked Questions
What is GeneSifter?
GeneSifter Lab Edition is an end-to-end lab management system for genetic analysis core and service labs. GeneSifter Analysis Edition is a genetic 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 genetic data.

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How can I buy GeneSifter?
Contact your account representative or call 1-800-762-4000 for information on purchasing GeneSifter Lab or Analysis Edition.

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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 types of analysis platforms can I analyze with GeneSifter?
GeneSifter accepts data from all commercial microarray platforms, as well as Next Generation DNA Sequencing (if converted to a Gene List) and 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 Analysis Edition 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. Customers with data in Gene List formats that they have obtained from a GeneSifter enabled core lab can also analyze those results using GeneSifter Analysis Edition. 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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