UCHSC Affymetrix Microarray Core Facility Website

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Microarray Data Analysis Tools Available in the Core

GeneChip® Operating Software (GCOS)

Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis. GCOS also supports the GeneChip® DNA Analysis Software (GDAS) for resequencing and genotyping data analysis and report generation.

Seamless Instrument Control
Accurate Data Analysis
Integrated Data Management
Readily Upgradeable to Client-Server Configurations
Supports Gene Expression, Resequencing and Genotyping Applications

GeneTraffic®/ArrayAssist

GeneTraffic® software from Iobion Informatics performs microarray data management and analysis. Through Internet Explorer on a desktop PC, you can access your data and projects from any location. To access GeneTraffic®, please register with core lab website to create a GeneTraffic® account for you, then click here to access the server.

Easily analyze GeneChip® microarray data with powerful statistical analyses, clustering, and visualization tools
state-of-the-art probe-level analyses greatly increases the precision, accuracy and sensitivity of GeneChip® expression data
Integrated, searchable database of current gene annotations for all GeneChip® microarrays, based on the latest NetAffx™ annotation

GeneSpring® cutting-edge tools for expression analysis

The Core has a GeneSpring® concurrent key server. Users can take advantage of our key server to use the software at lower cost. Affymetrix data can be imported into GeneSpring® to perform data visualization, validation, normalization, statistic analysis, and classification. Detailed information can be found on Silicon Genetics website.

Advanced Statistical Tools These include t-tests, 2-way ANOVA tests and 1-way post-hoc tests and class prediction tools.
Data Clustering Gene trees (hierarchical clustering), experiment trees, self-organizing maps, k-means, Principal Components Analysis (PCA) and QT clustering.
Visual Filtering Easy filters for entry-level users, advanced filtering for power users Real-time visual inspection of filtering results Automates complex tasks Standardizes important experimental SOPs
3D Data Visualization The 3D scatter plot tool provides in-depth and interactive representations of highly complex data.
Data Normalization Sixteen transformations are available for creating powerful and flexible normalization scenarios.
Pathway Views With the pathway viewer, genes and their expression patterns can be visually characterized based on their location within a cellular pathway. Users can design their own pathway diagrams or directly import publicly available pathway maps. Users can predict genes associated with discrete steps in the pathway of interest. Visualize KEGG general and organism-specific pathways Support for a large number of GenMAPP pathways
Search for Similar Samples GeneSpring allows you to compare the expression profile of a given sample to all of the other samples, even if they are derived from different experiments or aren't associated with any experiment at all.
Scripting Researchers can create custom scripts to automate repetitive analytical tasks, ensure consistency in the analysis process and simplify data analysis management.
MAGE-ML Export Export your experiments in MAGE-ML, the Micro Array Gene Expression Markup Language.

Ingenuity Pathways Analysis

The Ingenuity Pathways Knowledge Base is the world's largest curated database of biological networks created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. Using this knowledge base, bioinformaticians are developing genome-scale computational solutions to understanding biological mechanisms.

Integrated, broad coverage of systems biology including protein, gene, protein complex, cell, cellular component, tissue, organ, small molecule and disease interrelationships
Broad genome wide coverage of over 20,000 mammalian genes
Millions of pathway interactions extracted from literature
Semantic/linguistic consistency based on a comprehensive ontology with over 280,000 concepts, twenty-five times larger than other popular ontologies
Synonyms and homonyms maintain object identity and remove duplicate objects
Representation of biological context, including species specificity, localization, mutations, and experimental conditions
Systematic capture of canonical pathway relationships
Up to date with most recent literature

By helping researchers systematically analyze their experimental data in the context of biological pathways, the Ingenuity Pathways Knowledge Base provides value throughout the drug discovery process, from early stage target ID and validation, to later stage activities such as toxicology, pharmacogenomics, biomarker identification, and alternative indications of approved drugs.

Partek® Genomic Suite

Partek Genomics Suite is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noise. Designed for high-dimensional genomic studies containing thousands of samples, Partek Genomics Suite is fast, memory efficient and will analyze large data sets on a personal computer. It supports a complete workflow including convenient data access tools, identification and annotation of important biomarkers, and construction and validation of predictive diagnostic classification systems. Partek Genomics Suite is Affymetrix GeneChip-compatible™ for gene expression analysis, exon expression analysis, and chromosomal copy number analysis.

Microarray Data Analysis Tools Available in the Core

Other data analysis tools

Useful Data Analysis Resources