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GeneChip-compatible Software Providers

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GeneChip-compatible™ software providers

To get the most out of your microarray experiments, you need effective software tools to manage and analyze your data. As the applications for GeneChip® Arrays continue to grow in number, the available software tools also evolve in variety and scope. It's always helpful to have several applications to choose from, but such variety can present a challenging decision.

To help you select the right software tool for your needs, Affymetrix has collected a series of applications that provide the following advantages:

  • Seamless technical integration with native Affymetrix file formats
  • Integrated and up-to-date NetAffx® annotation information
  • Tighter integration of sample annotations with microarray data
  • Continued commitment to future technical integration as the Affymetrix platform evolves

GeneChip-compatible™ software applications are developed, sold, and supported by Affymetrix partners. Please contact the partner for more information about applications displaying the GeneChip-compatible™ logo.


GeneChip

Applications displaying the “SNP 6.0 Ready” logo can handle CHP files produced by Genotyping Console™ software using AGCC formats supporting data from the Genome-Wide Human SNP Array 5.0 and Human SNP Array 6.0.


Types of GeneChip-compatible™ Software

Because of the variety of informatics tools available for the Affymetrix platform, the compatible applications are divided into various application classes. Each application class has its own set of technical criteria to ensure compatibility.

  • Exon Expression
    Incorporating advancements in labeling the entire length of the transcript as well as increases in array density, exon expression arrays offer significantly greater resolution in monitoring expression within a biological system. Applications within this class provide gene- and exon-level data and offer the potential to predict alternatively spliced transcript forms.

  • Gene Expression
    These applications provide gene-level analysis solutions for Affymetrix gene expression arrays, including 3' arrays and the new Human Gene 1.0 ST Array, which measures the overall expression of all transcripts derived from a gene, not just the 3' end.

  • Regulation Analysis
    With unbiased GeneChip® Tiling Arrays and assays such as ChIP-on-chip, these applications can help you gain insight into the mechanisms of transcriptional regulation.

  • SNP Analysis
    You can identify genomic regions of linkage or association using these applications.

  • SNP Data Management
    These applications organize genotyping information generated by Affymetrix mapping assays coupled with family or co-variant sample attribute information, allowing you to link genotype and phenotype.

  • Chromosomal Copy Number
    Software applications within this class allow you to leverage Affymetrix arrays to identify differences in chromosomal copy number, thus providing insights into fields such as cancer biology.

  • DNA Sequence Analysis
    DNA sequence analysis tools offer analysis methods for data coming generated by Affymetrix DNA resequencing arrays and provide greater information about sequences represented on any class of Affymetrix microarrays.

  • Pathway/Network Analysis
    Providing the greatest biological insight, this set of applications leverages databases of published literature to perform the complex task of building and visualizing the potential interactions between gene products.

  • Expression Data Management
    This set of applications provides the necessary housekeeping functions associated with storing, managing and distributing the massive quantity of data generated by microarrays. These applications are focused on the expression assay and typically offer tightly integrated analysis functionality.

  • Laboratory Management
    This class of tools focuses on the upstream challenges associated with microarray experiments including sample tracking, reagent inventory and process flow.

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DNA - SNP Genotyping and CNV Analysis

SNP Analysis

These applications provide analysis solutions for Affymetrix genotyping arrays, which are used for genome-wide linkage or association studies. Starting with SNP calls, the bi-allelic state of a given SNP is indexed against its genomic location. By comparing the pattern of these SNP markers across multiple samples, as well as their association with phenotypic or clinical markers, regions of the genome are identified as relevant to a given trait.

SNP Data Management

Applications in the SNP data management category provide centralized storage of data generated by Affymetrix mapping assays and the necessary family or co-variant sample attribute data. Data reformatting is another hallmark of this class of tools due to the large variety of input data structures that exist in largely academic-based, genetic analysis programs.

Chromosomal Copy Number

Identification of chromosomal amplifications or deletions can be correlated with disease-associated phenotypic conditions. Software applications within this class allow researchers to leverage Affymetrix arrays to identify differences in chromosomal copy number thus providing insights into fields such as cancer biology.

Developers interested in creating tools in this application class should review the resources available here.

DNA Sequence Analysis

These applications serve as DNA sequence analysis tools for data generated by Affymetrix DNA resequencing arrays. They also provide more information about sequences represented on any class of Affymetrix microarrays.

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RNA - Gene Expression Profiling

Exon Expression

Exon analysis involves generating signal estimates from input CEL files at either the gene or exon level. Gene-level estimates can be leveraged using traditional expression workflows. Exon-level estimates can be combined using a variety of gene models used to predict potential transcript forms. Comparing how these forms might differ within a collection of samples leads to predictions of alternatively spliced transcripts. The dynamic nature of genome builds and annotation information used in gene models can increase the complexity of exon expression analysis. Applications within this category have been specifically built to handle these types of investigative questions.

Gene Expression

Supports Analysis of Whole-transcript Gene Expression

The following GeneChip-compatible™ applications can analyze whole transcript-based gene expression arrays, such as the Human Gene ST 1.0 Array, with data output to AGCC-formatted CHP files. If probe-level data (CEL files) are input, these applications support using dynamic probe group files (PGF) as library files. These applications compare expression arrays and generate lists of genes with significantly affected expression. Many applications support more complicated classification analyses that use expression signatures to differentiate samples into discrete groups correlating with phenotypes.

View a Summary Table >

Regulation Analysis

With the use of an antibody to a transcription factor of choice and Affymetrix’ ChIP-on-chip protocol, researchers can gain genome-wide information on the DNA binding pattern of that transcription factor or any DNA-binding protein. Use applications in the regulation analysis application class to help determine where a protein of interest is binding. Some applications that also might be GeneChip-compatible™ within the gene expression category will help to intersect these data with steady-state expression data.

Developers interested in creating tools in this application class should review the resources available here.

Expression Data Management

This set of applications provides the necessary housekeeping functions associated with storing, managing and distributing the massive quantity of gene expression data. These tools tend to focus on downstream management of Affymetrix data after the hybridization of the arrays. Data can be stored in flat files or in databases. Sample attributes are stored as well allowing quick searches for specific samples of interest. Often these applications are tightly integrated with analysis solutions from the same commercial provider.

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Pathway/Network Analysis

This set of applications performs the complex task of building and visualizing the potential interactions between gene products that leverage databases of published literature. Typically lists of affected genes from a completed microarray experiment are fed into these applications. This class of tools can provide the greatest biological insight to the end user due to the focus on visualizing the dynamic interactions between gene products and their spatial distribution within the cell.

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Laboratory Management

Larger in scope than the data management class, the laboratory management class provides informatics solutions to organize the vast number of assays and reagents that exist within the modern laboratory. This class of tools focuses on the upstream challenges associated with microarray experiments including sample tracking, reagent inventory and process flow. Typically these tools are applicable to general laboratory needs and are not inherently specific to microarray processing.

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