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 continues to evolve

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GeneChip-compatible Software	Copy Number	Exon Expression	Gene Expression	SNP Analysis	Regulation
Partek
Genomatix
JMP from SAS

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 with the Affymetrix GeneChip platform.

Exon Expression   Incorporating advancements in both labeling the entire length of the transcript and increases in array density, exon expression arrays offer significantly greater resolution in monitoring expression within a biological system. Applications within this class offer both gene-level and exon-level data as well as offer the potential to predict alternative spliced transcript forms. Gene Expression   These applications provide gene level analysis solutions for Affymetrix gene expression arrays including both 3' expression 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 of a gene. Regulation Analysis   Using unbiased GeneChip® Tiling Arrays and assays such as ChIP-on-chip, researchers can gain insights to mechanisms of transcriptional regulation using these GeneChip-compatible software applications. SNP Analysis   Users can identify genomic regions of linkage or association using the GeneChip-compatible™ Applications listed here. SNP Data Management   These applications organize genotyping information generated by Affymetrix Mapping Assays coupled with family or co-variant sample attribute information allowing genetic researchers to have the informatics tools to link genotype and phenotype. Chromosomal Copy Number   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. DNA Sequence Analysis   DNA sequence analysis tools offer analysis methods for data coming from Affymetrix DNA Resequencing arrays and provides greater information about sequences represented on any class of Affymetrix microarrays. Pathway/Network Analysis   Providing the greatest biological insight, this set of applications performs the complex task of building and visualizing the potential interactions between gene products leveraging databases of published literature. 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.