Affymetrix develops and markets technology for acquiring, analyzing, and managing complex genetic information for use in biomedical research.

BioConductor: Open Source Software for Bioinformatics is an open source and open development software project for the analysis and comprehension of genomic data.

DNA-Chip Analyzer (dChip) is a software program that applies model-based expression analysis of microarrays as well as conducts higher-level analysis procedures such as comparative analysis and hierarchical clustering (Li and Wong 2001a).

National Center for Biotechnology Information creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.

NetAffx enables researchers to correlate GeneChip® array results with array design and annotation information.

Oklahoma IDeA Network for Biomedical Research Excellence (OK INBRE) is the web site for the Oklahoma University Health Science Center's laboratory for genomics and bioinformatics.  The Laboratory for Genomics and Bioinformatics is a genomics facility offering DNA sequencing (custom and genome-scale projects), genotyping, microarray design, hybridization and data analysis, and other services.  Custom microarrays have been designed for several bacterial genomes, including Actinobacillus actinomycetemcomitans, Haemophilus ducreyi, Neisseria gonorrhoeae, Staphylococcus aureus, and Streptococcus pyogenes.  The OUHSC core facility offers microarray hybridization and data analysis services, and data archival using the open source BASE database format.  A free Perl workshop is periodically offered on the OUHSC campus to introduce interested individuals to the language and its use in bioinformatics.  Among the programming languages available, Perl is arguably the favorite of bioinformatics programmers. Its low learning curve and flexible syntax make it an ideal beginning language for biologists, and its unsurpassed text-parsing ability make it an excellent choice for data such as protein and nucleic acid sequences.  This informal, non-accredited workshop consists of four two-hour sessions spanning two weeks.  You will not walk away from these sessions a Perl expert, but you should have a working knowledge of the basic syntax of the language and programming structure that will help you carry on further self-study.  No previous programming experience is required.  The only prerequisites are an understanding of operating system usage in windows or linux, such as creating files and folders and using a text editor.  Very general knowledge of biological processes such as transcription and translation also will be assumed.  Class sizes will be small and students will follow the instructor on laptop computers provided by the workshop.

     Oklahoma Medical Research Foundation (OMRF) Microarray Research Facility Scientists at the OMRF Microarray Research Facility collaborate with researchers at OMRF and around the world to study differential gene expression in order to understand pathophysiologic states at the molecular levels.  They manufacture human, mouse, and  Candida albicans oligonucleotide microarrays, plus a variety of custom cDNA microarrays containing genes from libraries produced by individual investigators.  Links to gene lists on oligonucleotide arrays are available to download to your computer.  A variety of protocols, available online, have been developed and optimized at OMRF to assist investigators here and elsewhere in the use of microarrays.  The Microarray Facility Bioinformatics Section designs novel analytical tools for use in microarray studies, and assists users in analyzing and understanding microarray data obtained from experiments performed at the Facility.  Links to recent publications and public databases available for downloading to your computer are also listed.

      Oklahoma State University Microarray Core Facility The satellite facility at OSU consists of two interoperating units, the OSU Microarray Core Facility and BioinfOSU.  The OMCF has modern microarray printing, scanning and data analysis capabilities and provides consultation and training in the form of workshops in microarray analysis.  BioinfOSU supplies the OMCF with software for the analysis of microarray data, particularly the popular Gene Pix Autoprocessor (GPAP), a web-based application providing preprocessing of raw microarray data.  GPAP performs signal filtering, background correction and signal normalization and provides diagnostic plots and reports to evaluate data quality and the effects of preprocessing.  GPAP can also identify the top differentially expressed genes for the user.  In addition to supplying the supporting computer infrastructure for the OMCF efforts, BioinfOSU provides other bioinformatics resources to scientists.  It hosts the PipeOnline tool for processing and annotation of ESTs and VirOligo, a database of oligonucleotides used in virus detection.  A variety of software packages are provided for local users.

The R Project for Statistical Computing is a language and environment for statistical computing and graphics that interfaces with dChip to perform ANOVA gene filtering, to generate normalization plots, and to conduct linear discriminant analysis.

SAM: Significance Analysis of Microarrays is a software program that interfaces with Microsoft Excel to determine if the expression of any genes is significantly related to the response variable (e.g., treated vs. untreated).

Statistics for Microarray Analysis (SMA) are an R add-on package that conduct simple R functions for basic and discriminant analyses.

Unigene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.

      University of Oklahoma Microarray and Bioinformatics Core Facility The University of Oklahoma Bioinformatics Core Facility hosts a fully functionial, web-accessible microarray database, developed with funding from the NSF-EPSCoR and NIH-BRIN.  The OU Microarray Database (OUMDB) provides users of the Oklahoma Bioinformatics Network a web interface to upload, manage, and analyze microarray experiments.  The OU Microarray Core Facility provides equipment for microarray printing, hybridization and scanning.  The staff of the OU Bioinformatics Core includes skilled programmers who regularly tailor the database to accommodate user needs.  Specifically, the OUMDB provides password-protected access to features including a complete LIMS, array-design, data-upload interface, statistical package, experiment organization, and data-mining package.  The OU E. coli Gene Expression Database hosted by OUMDB offers the most extensive publicly accessible E. coli microarray datasets in the world.

The University of Tulsa is the home of the TU Microarray Core Facility.

The University of Tulsa College of Engineering and Natural Sciences is the school that houses the TU Microarray Core Facility.

The University of Tulsa Department of Biological Science is the department wherein the TU Microarray Core Facility is located.