We at Affymetrix understand that getting the most out of your experiments using GeneChip® Arrays depends on the available software tools to manage and analyze your microarray data. As the applications for Affymetrix GeneChip®
Arrays continue to grow in number, the available software tools also evolve in both variety and scope. Although it is always comforting to have the ability to choose
the right tools for the job, such a variety of informatics solutions represents yet another decision to research. To help you select the right software tool for your
needs, Affymetrix has collected below a series of applications.
Explore the Software Solutions Catalog
Applications which display the “AGCC Ready” logo can handle the new file formats used by both Affymetrix GeneChip Command Console (AGCC) and Expression Console.
APPLICATION CATEGORY - REGULATION ANALYSIS
With the use of an antibody to a transcription factor of choice and Affymetrix' ChIP on chip protocol, a researcher can gain genome wide information on the DNA binding pattern of that transcription factor or any DNA binding protein for that matter. Use applications in the Regulation Analysis application class to help determine where a protein of interest is binding. Some applications which also might be GeneChip-compatible within the Gene Expression Category will help you intersect these data with your steady-state expression data.
Developers interested in creating tools in this application class should review the resources available here.
Microarray analysis and annotation software working with Affymetrix raw data files. ChipInspector carries out significance analysis on the single tiling probe level. Tiling probes with significant expression values are annotated based on the Genomatix proprietary genome annotation and analysis system ElDorado. Based on the annotation result, probes are assigned to genomic regions. Several clustering features allow to group tiling probes with similar profiles. Direct links to Genomatix' BiblioSphere PE, ElDorado and GEMS Launcher enable the analysis of relations between expressed genes, discovery of synthenic regions as well as prediction and analysis of new gene loci and promoters.
View a recent GeneChip-compatible webcast illustrating analysis of the Human Promoter Tiling Dataset with SP1 transcription Factor.
Partek® Genomics Suite (Partek GS) provides easy to use workflows for tiling experiments including ChIP on Chip, methylation, and copy number estimation. Partek GS has been optimized to import, normalize, and analyze large scale Tiling studies on today's desktop and laptop computers. Partek GS provides statistical methods to automatically detect and display sites of protein/DNA interaction in ChIP on Chip experiments or regions of chromosomal copy number alterations. For any type of study, the researcher can select regions of interest and create lists of genes, SNPs, or sequences in those regions. Results are presented in interactive visualization and tabular format. Partek GS provides a single software solution with workflows to support analysis of all major Affymetrix GeneChip technologies. Partek is GeneChip-compatible for Expression, Exon, Copy Number, and Tiling Arrays.
View a recent GeneChip-compatible webcast illustrating analysis of the Human Promoter Tiling Dataset with SP1 transcription Factor.
