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.

Overview

To help you select the right software tool for your needs, we have 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.

Applications displaying the “SNP 6.0 Ready” logo can handle CHP files produced by GeneChip 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.

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.

HelixTree, the flagship product of Golden Helix’ SNP and Variation Suite, employs an unparalleled set of SNP analysis and genetic association tools offering more ways to uncover true genetic associations than any other programs. With citations in over 100 peer reviewed publications, HelixTree is recognized as the leading software application for targeted gene and whole-genome association studies.

Why HelixTree?

  • GeneChip-compatible: Directly import and analyze CHP files from Affymetrix GeneChip Human Mapping Arrays, including the Genome-Wide Human SNP Array 5.0 and SNP Array 6.0.
  • Comprehensive: Use an unparalleled set of tools for both population- and family-based association studies.
    • Streamline the import and management of large complex data sets with mixed variable types.
    • Calculate a host of summary statistics.
    • Assess and remedy data quality issues.
    • Conduct case/control, quantitative trait loci (QTL) and categorical-type analysis with numerous methods for allelic, genotypic, haplotypic, copy number variation, runs of homozygosity, multi-locus and regression-based association tests.
    • Detect genetic signals in the presence of confounding factors.
    • Control for false-positives.
    • Perform FBAT analysis and power calculations with an exclusively enhanced PBAT
    • Click here for a more complete feature list.

  • Fast and Efficient: Fast algorithms and sparse data storage technology optimize computational speed and memory usage, enabling truly interactive whole-genome analysis with conventional computing hardware. Need more speed? Certain analyses can take advantage of multi-core and multi-processor systems either locally or in a distributed grid environment using Condor® or the Univa UD’s Grid MP.
  • Easy to Use: A combination of intuitive wizards, superb data visualization tools, spreadsheets and scripting functions make HelixTree usable by both statistical geneticists and other life science experts.
  • Extensible: A fully programmatic Python scripting interface enables automation of workflows, incorporation of user-defined statistical methods and integration with other packages. HelixTree is currently integrated with the R and S-Plus statistical packages.
  • Proven: HelixTree has been cited in more than 100 peer-reviewed publications.

View a complete analysis workflow of data from the Affymetrix 500K Mapping Array Set

GenSense is an analysis and annotation software solution built on the InforSense Platform, designed for analyzing and annotating genome-wide association studies.

GeneChip compatibility in GenSense allows direct importing of CHP and ARR files from the SNP Array 5.0 and SNP Array 6.0 together with the associated NetAffx® information.

With the throughput enabled by the new Affymetrix genotyping platforms, delivering novel biomarkers is within reach. Whole-genome association studies are becoming commonplace so analytic software needs to be highly flexible to enable the ad hoc integration of algorithms and data for placing genome-wide association studies in a biological context.

Features include:

  • Work with large-volume data sets, including chips that measure up to 1 million SNPs across thousands of samples
  • Portal access for scientists and statisticians, which can be completely built and customized using workflows
  • Automated quality control to filter SNPs and samples based on genotype quality score, genotype completion and sample duplication
  • Statistical analysis of case control data: view the results with appropriate visualizations
  • Filter, sort and prioritize SNPs
  • Visualize case control test results as hit SNPs in a genome browser.
  • Pre-built, flexible connectors for third-party tools (e.g. PHASE, PLINK and HaploView) and scripts (e.g. R and Perl)
  • Link to phenotype data to find SNPs most highly associated with disease and/or drug response
  • Open SDK for developing and customizing analytics

JMP Genomics, a desktop statistics tool for SNP analysis, is an integrated environment for accessing and analyzing Affymetrix SNP data. It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS, and incorporates linkage disequilibrium analysis, whole-genome association analysis, and haplotype analysis using processes from SAS Genetics. In addition, loss of heterozygosity (LOH) and chromosomal copy number analyses can be performed on Affymetrix CNAT files using the partition tool in the JMP platform. The JMP for Genomics Suite also includes tools for proteomic and microarray analyses and other sophisticated statistical tools, providing a single application for all of your research

Partek Genomics Suite (Partek GS) is an integrated statistical and visual analysis solution for GeneChipexperiments that is optimized for fast and memory-efficient processing of large, ultra high-dimensional data.

Partek GS supports single SNP association tests performed on allele, genotype and dominant/recessive models. Genotype data can be analyzed using statistical tests such as Chi², Hardy-Weinberg Equilibrium and linkage disequilibrium. Get accurate estimation of p-values in even the smallest datasets using Monte Carlo tests. Explore data with tabular analysis as well as visual analysis tools including frequency plots, biplots and heat maps, which can be used to visualize linkage disequilibrium within the data. In addition, after identifying loci of interest, explore copy number and LOH data in the same region. Gene and SNP lists can be easily created and exported. Corresponding data can be seamlessly linked to and visualized with the mapping array data.

Struggling to manage and analyze genotyping data from various sources instead of focusing on the science behind your study?

The Rosetta Syllego System addresses the informatics challenges associated with conducting genetic studies. Set your study apart by bringing all of your data and results together in one easy-to-access repository. Designed for biologists, statistical geneticists, and investigators responsible for generating genotyping data, the Syllego System enables you to:

  • Align your scientific question with your genotyping technologies and data sources. Cleverly designed tools help you better plan and execute genetic studies across a variety of genotyping platforms and data sources.
  • Generate high-quality data that does not cloud downstream analyses. User-defined statistical cuts and quality-control checks minimize loss of time in downstream analyses. Quality-Control results can be used to merge or refine relevant study data into analysis data sets targeted for further analysis.
  • Use your analysis methods of choice. You can easily select and combine your relevant genotype and phenotype data to interface with the analysis environment of your choice, including PLINK and "R" and then easily visualize and share your results and methods.
  • Maximize the return on your genetic study. The Syllego System gives you the tools to not only analyze your current study, but also catalog your study data and analysis results for use with public and privately available genotype data, future studies and collaboration efforts.

Put your genetic data management and analysis challenges behind you. Discover the Rosetta Syllego™ System.

Exemplar Analytics is the leading tool for performing genome-wide association studies with major publications in Nature Genetics. Exemplar has the most comprehensive set of analyses found in any product on the market and has proven itself an invaluable discovery tool at leading pharmaceuticals and research institutes. Features include:

  • GeneChip-compatible
    • Wizard-driven import of CHP/CEL files with complete support of Affymetrix Genome-Wide Human SNP Arrays.
  • The most comprehensive association statistics
    • Chi Square, OR, RR, Fishers Exact, Armitage Trend Test and more.
    • World’s fastest multiple testing corrections: Permutation, FDR and Bonferroni.
    • TDT and haplotype relative risk for triad analysis.
  • Principal component analysis for admixture corrections
    • Identifies and corrects for hidden sub-groups in genome-wide association studies.
  • Haplotype analysis
    • EM algorithm inference of haplotype frequencies and p-value of association.
    • Sliding window across whole genome.
  • Copy number variation analysis
    • Finds insertions/deletions in the genome and graphically displays results.
    • Loss of heterozygosity analysis.
  • Quantitative trait analysis
    • Predict traits from genetic and non-genetic factors.
    • ANOVA, linear and multiple regression.
  • Multi-locus modeling
    • Uses advanced machine learning to discover multi-locus models that correspond with phenotypes.
    • Cited in landmark paper on AMD in Nature Genetics.
  • Genetics database and annotations
    • Complete dBSNP, human gene and gene ontology database shipped with product.
    • Maps significant SNPs to their related genes and ontological information with one click.
  • Whole-genome viewer
    • Layer 10K, 50K and 500K Array results on one view of the whole genome.
    • Mix and match different analyses in one view.
    • SNP-level annotations with related genes, positional info, etc.
  • High performance, high scalability
    • Designed to take advantage of today’s dual- and quad-core processors to accelerate discoveries.
    • Process thousands of samples of data generated by the SNP Array 5.0 and SNP Array 6.0.

Exemplar Analytics can be evaluated with a free demonstration version upon request. For those needing assistance with data analysis, Sapio Consulting Services has four years of experience conducting genome-wide association studies with leading institutions including the NCI, NICHD, Cleveland Clinic and Children’s Hospital of Philadelphia. For more information on these products or services, please email sales@sapiosciences.com

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.

Biocomputing Platforms’ BC/GENE is a database environment designed to combine genotype data with phenotypes, maps and pedigrees and to create a productive statistical analysis pipeline. The platform has been designed to handle the output of modern high-throughput SNP genotyping technologies. BC/GENE enhances the use of the best genetic analysis programs by utilizing a web browser interface to set up analysis runs and generating input files automatically. BC/GENE also features a queue system for running multiple calculation tasks. Additional analysis tools and programs can be integrated into the system.

Biocomputing Platforms’ BC/SNPmax is a data management solution for whole-genome association studies. It integrates high-density SNP genotype data with phenotypes and maps, creating a highly productive data analysis pipeline with automated input file generation for analysis programs.

BC/SNPmax enhances the use of the best analysis programs for quality control, case/control analysis and family-based analysis. An advanced built-in queue system supports performing multiple, large parallel database transactions and calculation tasks. The queue system also makes it easier to build powerful calculation clusters.

Progeny Lab is a data management tool designed for large-scale genome-wide scans or specific target regions for linkage-type analysis or association studies. Comprehensive management includes:

  • All variations of Affymetrix SNP sets (10K, 100K, 500K, etc.)
  • High-speed imports of native Affymetrix CHP file genotypes or GDAS text outputs
  • Automated error checking of genotype imports including Mendelian errors
  • Custom exports to multiple analysis platforms
  • Fully functional sample tracking
  • Customizable database tracks both pedigrees and individuals, allowing unlimited custom data fields
  • Functionality to manage all clinical and lab data in one relational database

View a recent GeneChip-compatible webcast illustrating how Progeny Lab can aid in data management from the GeneChip Human Mapping 500K Array Set

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.

Nexus Copy Number allows scientists to perform copy number analysis and visualization across large data sets that have thousands of samples and millions of probes per sample. The software supports many platforms including Affymetrix SNP array data. Nexus Copy Number provides an intuitive and interactive user interface that allows rapid identification of critical regions of genomic change in the entire population or sub-groups (e.g. different disease states). The publication-quality visualization tools are coupled with sophisticated statistical analysis for identification of areas of minimal overlap, statistically significant regions between two populations, clustering of samples based on genomic profiles, over representation of GO terms in regions of genomic instability, and much more. Nexus Copy Number is unlike any other tool for copy number analysis on the market due to BioDiscovery’s decade-long experience in developing pioneering software for the microarray market.

Exemplar Copy Number Module is the first complete implementation of the copy number algorithm outside of the Copy Number Analysis Tool (CNAT). Exemplar has the following features:

  • Highly scalable to the 500K Array.
  • Full reference set generation capability (RefGen).
  • Includes reference sets for 10K to 500K Arrays.
  • High performance – five times faster on RefGen and two times faster on copy number analysis.
  • Whole-Genome Viewer that can mix and match the following in one integrated view:
    • 10K, 50K, 100K, 250K and 500K Array results
    • Results from other Exemplar modules like statistical analyses
    • Loss of heterozygosity results
    • Imported results from third-party tools like CNAG, dChip, R, etc.
    • CNT import from CNAT
  • Annotations of related genes, positional info from built-in, auto-updated genomics database
  • Advanced filtering of results on value ranges or standard deviation from the mean
  • Automatic, real-time gene ontology annotations

The Golden Helix’ Copy Number Analysis Module (CNAM) is an advanced software application which provides the high accuracy needed for whole genome copy number association studies.

CNAM provides a powerful set of novel methods and workflows for detecting copy number variations (CNVs) and performing association analysis on both CNV covariates and log ratios directly. It employs a proprietary optimal segmenting algorithm that can detect CNVs with astonishing accuracy. In fact, its unique multivariate method can detect CNVs at single marker resolution! You can also use CNAM to normalize log ratios against a reference set of your choice and correct for batch effects and stratification in your data using an Eigenstrat-based principal component analysis method.

Affymetrix compatibility
CNAM substantially replicates the Affymetrix workflow for converting CEL files to log ratios. This includes:

  • Quantile normalization (without gender bias)
  • Virtual Array Generation (merging CN and SNP data, or NSP and STY)
  • Normalizing log ratios against any reference population

This can be done for 500k, SNP 5.0, and SNP 6.0 arrays

CGH Fusion and oneClickCGH from infoQuant make copy number analysis for virtual karyotyping fast and easy. With infoQuant, you will have fully automated data analysis for CNV and LOH coupled with the convenience of fully integrated annotations. infoQuant's statistical algorithms have been specifically developed and validated for robust DNA aberration detection, including recognition of all allele-specific copy number changes. As such, all chromosomal anomalies are discovered, captured, and visualized in a fully automated, highly productive manner. You can even perform copy number analysis across hundreds and thousands of samples at the same time. Plus, when your analysis is complete, you will be able to visualize and report your findings via a variety of options, procedures, and formats. Annual licensing is flexible by design to meet the needs of the individual user as well as that of the most demanding, high-throughput laboratory environment. Both products are covered by infoQuant's world-class training and support team at no additional charge. Visit www.infoquant.com to learn more.

View a recent white paper on the Affymetrix SNP 6.0 using infoQuant's CGH Fusion®.

Partek Genomics Suite is an integrated statistical and visual analysis solution for GeneChip experiments, optimized for fast and memory-efficient processing of large, ultra-high-dimensional data. Statistical and visual features make it easy to detect regions of insertions and deletions on the genome. The Partek Genome Browser™ provides dot plots, box and whiskers, profiles and gene summaries to show the level of insertion/deletion and the number of affected individuals. All graphs can be exported in a publication-quality vector graphic format. Partek GS has seamless integration with CNAT version 3 output files and CEL files, and automatically associates annotations to all results, providing hyperlinks to the NetAffx Analysis Center and other Internet databases.

View a recent Partek webinar from October 2007 that illustrates a complete workflow to identify regions of amplification and deletion using the Affymetrix copy number platform.

 

 

 

 

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.

The Biotique Local Integration System (BLIS) is an R&D enterprise integration solution that provides a web accessible environment for integrating, analyzing and sharing knowledge assets. BLIS brings together people, projects, disparate data sources and workflow applications. Furthermore, BLIS integrates biological data in the public domain with in-house proprietary (subscribed) databases, commercial and custom micro array designs, and NetAffx annotations.

Designed for research executives, scientists and informatics experts alike, BLIS and its modules are licensed by more than 60 percent of large pharmaceutical corporations, more than 20 percent of small to medium-size pharmaceutical corporations, and two of the top 15 chemical companies

For the biologist who needs timely and comprehensive microarray annotation reports, GenomeQuest dramatically reduces the time spent searching databases and conducting sequence comparisons on entire lists of sequences. Its intuitive, easy-to-use software enables you to conduct your own searches, obtain best-fit answers to the search criteria you specify, and easily share your work with colleagues. GenomeQuest applies large-scale biological alignment methods to aid biological understanding based on the evolutionary linkage between two or more sequences. Built-in results analysis capabilities allow selection, sorting and filtering of huge data sets of alignments and annotations based on species, gene names, protein families and other scientific understanding linked to sequences and their annotations.

GenomeQuest integrates Affymetrix probe and target libraries for human, mouse and rat whole-genome array annotations with a worldwide network of transcript reference databases. Detailed reports are created automatically and can be published using Microsoft Office® or uploaded to popular microarray analysis packages. The system maintains continuous surveillance for new sequence information and sends email alerts to users when there is new information to discover. GenomeQuest is offered as a hosted ASP service or can be installed on customer servers providing security and integration with in-house data sets while requiring minimal administration. The system automatically updates itself with new sequence data from worldwide sequence repositories.

ElDorado is a genome annotation and analysis system with up-to-date annotations for more than 12 different organisms, comparative genomics (patent-pending) and the worlds largest quality-checked promoter annotation. Input sequences (mRNA/genomic) are mapped to all genomes in seconds including splice site predictions. Promoter sequences of regulated transcripts identified by ChipInspector can be extracted for further analysis. Effects of SNPs in promoter regions on transcription factor binding are annotated based on Genomatix’ MatInspector’s with its unique transcription factor binding site database. A direct link to Genomatix’ sophisticated gene regulation tools enables users to start sequence analysis right from the annotation.

GEMS Launcher is a software and database package that analyzes gene regulatory mechanisms on the molecular level. GEMS Launcher includes more than 20 different software tools for promoter analysis, high-quality data on transcription factor binding sites (TFBS), promoter modules and a gateway to the worlds largest database of quality-assessed mammalian promoters. The tools detect common organization in promoters of transcripts identified by ChipInspector. They search the promoter database for these motifs to detect additional potentially co-regulated genes, thereby facilitating the design of target verification experiments. The tools using TFBS predictions are based on the gold-standard MatInspector which is included in the package.

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.

XRAY is the only available Excel add-in for expression that can rapidly normalize and analyze large numbers of (binary XDA format) CEL files. XRAY is also unique in that it simultaneously implements gene-level and exon (alternative splicing) studies, while simultaneously using all 6 million probes at every stage of analysis. All controls and results are in Excel so users should be familiar with the controls and worksheet project organization.

  • Mixed-model ANOVA detects differential alternative splicing and gene expression even when data has dependencies.
  • Project construction wizard and use of the familiar Excel interface that allows users to work immediately with little software product training.
  • Runs on regular desktop and laptop computers (at least 700 MHZ with 500 MB RAM).
  • Fixed-memory implementation means that practically unlimited numbers of CEL files can be analyzed simultaneously.
  • Powerful enough to handle all the data on a chip with no filtering (but DABG and probe set annotation-level filters are available).
  • The only system that simultaneously shows genomic, transcript cluster, probe-set, probe annotation and expression in a single view.
  • Provides automatic annotation and links to public and NetAffx® databases.
  • Validates statistical analysis.
  • Efficient-quantile normalization and expression analysis for 20 CEL files runs in around 10 minutes on standard desktop computers (the application never requires more than 250MB RAM).

For more information or to contact sales directly, please call 775-787-9902 or email xray@biotiquesystems.com.

View a pre-recorded product demo on XRay v2.2, created in March 2007 (10 minutes)

View a recent GeneChip-compatible webcast illustrating analysis of the Human Exon Colon Cancer Data Set.

New XRAY demos for exon-expression analysis

View a two-minute demonstration of a typical workflow using Biotique’s XRAY for the analysis of GeneChip Exon Arrays (2:12)

Windows Media Player | Quicktime

View a two-minute demonstration on the interpretation of GeneChip Exon Array data from Biotique’s XRAY (2:30)

Windows Media Player | Quicktime

Expressionist | Support | Genedata

Genedata Expressionist® is a flexible, enterprise solution that manages, processes, analyzes, and visualizes omics data of unlimited size, including the complete transcriptome, genome, methylome, proteome, or metabolome. Its integrated mapping technology supports biological interpretation of the most complex data sets while facilitating decision making. Genedata Expressionist provides a single-point-of-access system for experimental, proprietary, and public data, including sample information, raw, and pre-processed data. Combining analysis results with reports and documentation, the system helps to bridge the gap between biology and statistics by making advanced statistical tools accessible to a wide range of users. Collaboration through session sharing and graphical analysis workflows gives interdisciplinary teams a platform on which to communicate, discuss, and interpret the results of biological experiments.

Genedata Expressionist for Microarrays evaluates GeneChip Exon Arrays for quality issues and flags potential outliers. Graphical workflows automate and streamline labor-intensive data pre-processing steps. These steps combine established algorithms such as MAS 5.0 or RMA, including background subtraction, condensing of probe intensities and different normalization methods.

Genedata Expressionist for Microarrays empowers all users to use sophisticated statistical tools for transcriptomics data analysis by combining carefully selected settings with guided workflows and layered help. Refined classification and clustering methods help to answer even the most challenging modern life science questions. Integration with popular pathway analysis packages (e.g., GeneGo MetaCore™ and Ingenuity Pathways Analysis™) complements the statistical analysis.

Genedata Expressionist for Microarrays includes fully interactive viewers to access and understand the results of complex statistical analyses and biological interpretation. With viewers, users can simultaneously select information from multiple graphs to facilitate and support interactive data exploration.

 

Support | Sales | Genomatix

A microarray analysis and annotation software that works with Affymetrix raw data files. ChipInspector carries out significance analysis on the single-exon probe level. Exon probes with significant expression ratios are annotated based on the Genomatix' proprietary genome annotation and analysis system ElDorado. Based on the annotation result, probes are assigned to transcripts. Graphical representations of the gene loci, include the display of alternative transcripts as well as probe-to-exon mapping. Particularly when analyzing exon arrays, this allows identification of differentially regulated transcripts and potential new splice variants. Several clustering features allow the grouping of exon probes with similar profiles. Results can be easily be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.

View a GeneChip-compatible webcast illustrating analysis of the Human Exon Colon Cancer Data Set.

GenoSplice | Example of Exon Array Analysis | Sales | GenoSplice's EASANA®

GenoSplice's EASANA® is an integrated solution for analysis, visualization and biological interpretation of Affymetrix expression microarray data, in particular Exon 1.0 ST Array data (EASANA® can also analyze data from the other Affymetrix expression microarrays, including 3' IVT and Gene 1.0 ST Array).

Thanks to six years of development within biology teams from the Network of Excellence on Alternative Splicing (EURASNET), EASANA® allows biologists to rapidly and easily find relevant results and enables the gene expression regulation study at both the gene and exon level.

EASANA® provides:

  • Quality control assessment of data
  • Lists of regulated genes and exons (with many links to classical databases including UCSC, Ensembl, NCBI, and also a direct link to the EASANA® visualization module, see below)
  • Pathway analysis (significant KEGG pathways where regulated genes are involved)
  • Hierarchical clustering of regulated genes
  • Analysis of expressed/regulated splicing factors

In addition, EASANA® provides a visualization module that displays the exon/intron structure of the genes with the different known alternative events and the probe localization, expression, and regulation. It allows users to:

  • Check results from the lists (genes and exons lists)
  • Facilitate the biological interpretation of results
  • Visualize any genes even if they are not found statistically relevant by the analysis
  • Share your results with collaborators

EASANA® is based on the annotations of the FAST DB® Client Edition. This database gathers all the information regarding gene products for human and mouse.

EASANA® is an intuitive interactive interface that greatly facilitates rapid identification of alternative transcripts from array data sets.

Trial Download | Features | Sales | Support | Home Page

Array Studio is a software package which provides state of the art statistics and visualization for the analysis of high dimensional quantification data (e.g. Microarray data) and genotype data (e.g SNP data). The software is designed for ease of use so that biologists can function at near the level of informatics specialists. Array Studio provides a fast, easy, and powerful solution for -omic data analysis.

Early versions of Array Studio have been used by over 200 industrial users in the past three years. More than 300 features in version 2.0 have been implemented based on feedback by those users.

Array Studio can be used for:

  1. Affymetrix data QC, analysis and visualization (3’ IVT, exon or gene arrays, SNP arrays)
  2. SNP/Genotyping analysis (Case/Control , Quantitative Trait , Categorical Trait , Stratified Trait, and Survival Trait Association Analysis)
  3. GEO data importing, QC, analysis and visualization
  4. General high dimensional data analysis, visualization, and manipulation
  5. High dimensional data management
  6. General data visualization and data manipulation

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek Genomics Suite is an integrated statistical and visual analysis solution for GeneChip experiments, optimized for fast and memory-efficient processing of large, ultra-high-dimensional data. Proven, rigorously tested statistical methods are integrated with 2D and 3D interactive visualization allowing users to reliably explore, identify and present important patterns in their data. The Partek Genome Browser™ provides dot plots, box and whiskers, profiles, exon-level, gene-level and alternative splicing summaries. All graphs can be exported in a publication-quality vector graphic format. Multiple classification methods are integrated with gene selection for accurate diagnostic/prognostic prediction. Seamless integration with CEL, .CDF, CHP, and .EXP files includes fast, memory-efficient RMA and probe-level import. Partek GS automatically annotates all results and provides hyperlinks to NetAffx and other internet databases.

View a GeneChip-compatible webcast that illustrates an analysis of the Human Exon Colon Cancer Data Set.

New Partek demo for exon expression analysis

View a brief demonstration of Partek Genomics Suite for the analysis of GeneChip Exon Arrays.

Windows Media Player | Quicktime

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.

ArrayStar® | Support | Sales | DNASTAR® | Download Trial

ArrayStar® is a desktop gene expression analysis software package designed to work with normalized Affymetrix GeneChip expression data files. The easy-to-use software provides users with state-of-the-art visualization and statistical analysis tools that are useful in monitoring expression-level changes throughout your experiments and in recognizing co-regulation patterns. Clustering of data with both heat maps and k-Means methods can be performed. A wide range of filtering tools permits users to quickly explore numerous research options. Easily imported NetAffxgene annotations provide the latest annotation information. The software is fully compatible with Windows Vista™ and XP. It is sold with the same type of perpetual license that DNASTAR® has used to sell its sequence analysis software for 24 years. A no-charge, 30-day trial version of the software can be obtained by contacting DNASTAR® at 608-258-7420 or visiting www.dnastar.com.

Biotique Systems | Support

XRAY is an affordable, powerful analysis tool for gene-level analysis of the new Human Gene ST 1.0 Array as well as analysis of all exon-level Affymetrix arrays. XRAY is a Microsoft Excel plug-in allowing you to work in the comfortable environment of Microsoft Excel and leverage tight integration with Microsoft PowerPoint and Microsoft Work. If you're a new user a wizard-driven import engine allows you to quickly enter data and automated analysis tracking autopopulates a Microsoft Word document allowing you complete documentation of your methods.

View a pre-recorded demonstration of data analysis from the Human Gene ST 1.0 Array. (7 1/2 minutes)

Expressionist | Support | Genedata

Genedata Expressionist® is a flexible, enterprise solution that manages, processes, analyzes, and visualizes omics data of unlimited size, including the complete transcriptome, genome, methylome, proteome or metabolome. Its integrated mapping technology supports biological interpretation of the most complex data sets while facilitating decision making. Genedata Expressionist provides a single-point-of-access system for experimental, proprietary and public data, including sample information, raw and pre-processed data. Combining analysis results with reports and documentation, the system helps to bridge the gap between biology and statistics by making advanced statistical tools accessible to a wide range of users. Collaboration through session sharing and graphical analysis workflows gives interdisciplinary teams a platform on which to communicate, discuss and interpret the results of biological experiments.

Genedata Expressionist for Microarrays evaluates GeneChip Exon Arrays for quality issues and flags potential outliers. Graphical workflows automate and streamline labor-intensive data pre-processing steps. These steps combine established algorithms such as MAS 5.0 or RMA, including background subtraction, condensing of probe intensities and different normalization methods.

Genedata Expressionist for Microarrays empowers all users to use sophisticated statistical tools for transcriptomics data analysis by combining carefully selected settings with guided workflows and layered help. Refined classification and clustering methods help to answer even the most challenging modern life science questions. Integration with popular pathway analysis packages (e.g., GeneGo MetaCore™ and Ingenuity Pathways Analysis™) complements the statistical analysis.

Genedata Expressionist for Microarrays includes fully interactive viewers to access and understand the results of complex statistical analyses and biological interpretation. With viewers, users can simultaneously select information from multiple graphs to facilitate and support interactive data exploration.

Support | Sales | Genomatix

ChipInspector is a microarray analysis and annotation software that works with Affymetrix raw data files. ChipInspector carries out significance analysis on the single-probe level. Probes with significant expression ratios are annotated based on the Genomatix proprietary genome annotation and analysis system ElDorado. Based on the annotation result, probes are assigned to transcripts. Graphical representations of the gene loci, featuring alternative transcripts as well as probe-to-transcript mapping, enable identification of differentially regulated transcripts, particularly when using exon arrays. Several clustering features allow the grouping of probes with similar profiles. Results can be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.

GenoSplice | Example of Exon Array Analysis | Sales | GenoSplice's EASANA®

GenoSplice's EASANA® is an integrated solution for analysis, visualization, and biological interpretation of Affymetrix expression microarray data, in particular Exon 1.0 ST Array data (EASANA® can also analyze data from the other Affymetrix expression microarrays, including 3' IVT and Gene 1.0 ST Array).

Thanks to six years of development within biology teams from the Network of Excellence on Alternative Splicing (EURASNET), EASANA® allows biologists to rapidly and easily find relevant results and enables the gene expression regulation study at both the gene and exon level.

EASANA® provides:

  • Quality control assessment of data
  • Lists of regulated genes and exons (with many links to classical databases including UCSC, Ensembl, NCBI, and also a direct link to the EASANA® visualization module, see below)
  • Pathway analysis (significant KEGG pathways where regulated genes are involved)
  • Hierarchical clustering of regulated genes
  • Analysis of expressed/regulated splicing factors

In addition, EASANA® provides a visualization module that displays the exon/intron structure of the genes with the different known alternative events and the probe localization, expression, and regulation. It allows users to:

  • Check results from the lists (genes and exons lists)
  • Facilitate the biological interpretation of results
  • Visualize any genes even if they are not found statistically relevant by the analysis
  • Share your results with collaborators

EASANA® is based on the annotations of the FAST DB® Client Edition. This database gathers all the information regarding gene products for human and mouse.

EASANA® is an intuitive interactive interface that greatly facilitates rapid identification of alternative transcripts from array data sets.

Sales

OmicsOffice™ for TIBCO Spotfire™ provides an analytic environment for scientific exploration and analysis of genomic expression data, which facilitates the identification of statistically meaningful results, expression patterns, and biologically-relevant insights. Dynamic linked visualizations coupled with the ability to interactively filter your results ensure an optimal end-user experience, answers to questions on demand, and unmatched breadth of insight.

A series of step-by-step workflows guide the analysis from start to finish, integrating advanced statistics and interactive visualizations to extract significant biological signals. This enables users of all levels to produce meaningful and reliable results. Each guided workflow contains a unique configuration of data access, quality control, analysis tools, and process support for specific expression platforms, allowing fast, informed decision-making. Workflows promote consistency and best practices while allowing maximum flexibility in analysis.

JMP® Microarray | Support | Sales | Home Page

JMP® Microarray, a desktop statistics tool for analyzing RNA expression, is an integrated environment for accessing, subsetting, analyzing, and exploring data patterns that can lead to the identification of promising new drugs. It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS. More than 85 genomics processes employ JMP’s Scripting Language (JSL) to launch open and customizable SAS macro programs in the background, enabling unparalleled data processing and statistical capabilities for rigorously understanding patterns and discoveries. JMP® Microarray offers proven Design of Experiments (DOE) tools for creating efficient and unconfounded experiments; a wide range of input processes for popular genomic instrumentation; deep and broad statistical methods that optimize tradeoffs between sensitivity and specificity; and integrated links to many current bioinformatics annotation tools and websites.

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek Genomics Suite is an integrated statistical and visual analysis solution for GeneChip experiments, optimized for fast and memory-efficient processing of large, ultra high-dimensional data. Proven, rigorously tested statistical methods are integrated with 2D and 3D interactive visualization allowing users to reliably explore, identify and present important patterns in their data. All graphs can be exported in a publication-quality vector graphic format. Multiple classification methods are integrated with gene selection for accurate diagnostic/prognostic prediction. Seamless integration with CEL, CDF, CHP, and EXP files includes fast, memory-efficient RMA and probe-level import. Partek GS automatically annotates all results and provides hyperlinks to NetAffx Analysis Center and other internet databases.

View a recent webcast from Partek that illustrates methods to perform cancer classification and survival analysis.

Qlucore | Download | Sales | Support | Technical Specs

With Qlucore Gene Expression Explorer (GEE) you quickly find patterns and structure in large data sets. GEE is easy to use and is yet a powerful tool for data exploration. Data is continuously visualized in 3D to give you instant feedback on your actions. The software is extremely fast. All results are shown immediately on a normal PC for data sets sized 500 x 100,000. You can perform advanced statistical analysis with just a few mouse clicks. You get continuous feedback on false discovery rates (FDR) and p-values for all genes. Paired data is handled with just two mouse clicks. GEE supports direct import of CHP files.

Supports analysis of 3’ gene expression

This set of applications provides analysis solutions for Affymetrix 3’-based gene expression arrays including the Human U133 Plus 2.0 Array. Starting with data at either the probe (CEL file) or probe-set level (CHP file), data summaries are generated and a variety of statistical methods are applied resulting in lists of differentially regulated genes. A variety of methods can be applied for data visualization. Genomic annotations are often intersected with expression data thus aiding the researcher in gaining biological insight from quantitative patterns of RNA levels within the cell.

 

GeneMaths XT | Technical Specs | Support | Sales | Applied Maths

GeneMaths XT is perhaps the most versatile software for microarray expression analysis available today. Its advanced concept of layers and subsets literally gives an extra dimension to expression analysis by making it possible to handle multiple data outputs (e.g. repeats, standard deviations, error values, etc.) as well as multiple subsets of genes and/or arrays. The software uses full error handling through all analysis, mining and statistics functions. Through its “Active History” concept, all steps of the analysis are recorded as scripts and can be repeated on other experiments. GeneMaths XT offers reliable normalization, interactive querying, pattern matching, time-course analysis and a wide range of mining, clustering and classification techniques. A rich set of statistical tools, presented in well-documented wizards, allows even non-experts to perform reliable hypothesis testing. All functions are designed for data sets of any size and are presented in an intuitive interface with powerful visualization tools. For the advanced user, GeneMaths XT is fully scriptable.

Register for a free trial of GeneMaths XT

 

Biotique Systems | Support

XRAY is an affordable, powerful analysis tool for gene-level analysis of the new Human Gene ST 1.0 Array as well as analysis of all exon-level Affymetrix arrays. XRAY is a Microsoft™ Excel plug-in allowing you to work in the comfortable environment of Microsoft Excel and leverage tight integration with Microsoft PowerPoint and Microsoft Word. If you're a new user a wizard-driven import engine allows you to quickly enter data and automated analysis tracking autopopulates a Microsoft Word document allowing you complete documentation of your methods.

View a pre-recorded demonstration of data analysis from the Human Gene ST 1.0 Array. 7 1/2 minutes

Istech | GenPlex | Support | Sales

GenPlex is an integrated software program for analyzing data from DNA microarray experiments using state-of-the-art statistical and mathematical algorithms. It provides powerful statistics, visualization and gene annotations in a user-friendly manner.

GenPlex performs various statistical analyses through five modules: Preprocessing, DEG Finding, Clustering, Classification, and Pathway Analysis. Two or multi-class analyses are possible using various parametric or non-parametric statistics in finding differentially expressed genes. Genes showing similar expression patterns can be grouped using hierarchical, K-means and SOM algorithms. Discrimination of different classes is implemented using KNN, multi FLDA and other methods. Analysis is driven by a wizard-style interface. Cross talk among different algorithms in different analysis modules provides users more stable and reliable results. GenPlex also supports biological annotation and automatic mapping of genes to pathways. The software provides an all-in-one solution where the user can easily obtain the best distinction error estimation.

Genowiz | Technical Specs | Support | Sales | Ocimum Biosolutions

Genowiz is a powerful gene expression analysis package for storing, processing and visualizing gene expression data efficiently. It includes a suite of advanced analysis methods and allows you to select analysis methods appropriate for your data set. Genowiz supports the upload of both cDNA and Affymetrix data (CDF, CHP and CEL files) and annotates the data using NetAffx annotations and information from various databases. Support for probe-level analysis algorithms like MAS 5.0 and RMA is provided. Genowiz allows you to update NetAffx annotations, providing the flexibility to view up-to-date annotations for genes. Genowiz has a wide range of statistical options for data normalization, transformation and filtration to provide a deeper and reliable insight into biological relevance of expression data. The application also comes equipped with several data analysis options like clustering, classification techniques, MIAME, gene ontology and pathways. Complete with excellent graphic visualization, it is an excellent tool for interpretation of biologically meaningful results. Genowiz is compatible with Windows, Linux and Mac operating systems.

Register for a free trial of Genowiz.

Trial Download | Features | Sales | Support | Home Page

Array Studio is a software package which provides state of the art statistics and visualization for the analysis of high dimensional quantification data (e.g. Microarray data) and genotype data (e.g SNP data). The software is designed for ease of use so that biologists can function at near the level of informatics specialists. Array Studio provides a fast, easy, and powerful solution for -omic data analysis.

Early versions of Array Studio have been used by over 200 industrial users in the past three years. More than 300 features in version 2.0 have been implemented based on feedback by those users.

Array Studio can be used for:

  1. Affymetrix data QC, analysis and visualization (3’ IVT, exon or gene arrays, SNP arrays)
  2. SNP/Genotyping analysis (Case/Control , Quantitative Trait , Categorical Trait , Stratified Trait, and Survival Trait Association Analysis)
  3. GEO data importing, QC, analysis and visualization
  4. General high dimensional data analysis, visualization, and manipulation
  5. High dimensional data management
  6. General data visualization and data manipulation

DecisionSite for Functional Genomics | Technical Specs | Support | Sales | Spotfire Inc.

Spotfire’s DecisionSite for Functional Genomics offers scientists a powerful visual analytic environment for exploring and finding unexpected relationships in gene expression and other types of genomic data. To better understand the large amounts of data from microarray experiments, rt-PCR and proteomic studies, DecisionSite for Functional Genomics provides rapid normalization, interactive filtering, clustering and statistical capabilities that give scientists deeper, more reliable insights into the biological relevance of the data. DecisionSite for Functional Genomics provides direct access to Affymetrix databases and CHP files, NetAffx files and a number of other data sources.

GeneSifter | Technical Specs | Support | Sales | Geospiza

GeneSifter the only microarray data analysis system optimized for biomedical research, won the 2005 “Best Practices Award for Product Innovation” in Bioinformatics in Drug Discovery from Frost & Sullivan. They noted that ”the flexible nature of web-based GeneSifter enables scientists to better understand the biology behind their gene expression data,“ and that scientists using GeneSifter products have testified to improved research, savings in training time, reduction in costs, and faster results. The GeneSifter product line includes GeneSifter Lab Edition, for individual researchers; GeneSifter Core Edition, for core facilities that prefer to administer their own accounts while taking advantage of GeneSifter's lower training and support costs; GeneSifter JumpStart, for scientists seeking to accelerate initial analysis efforts; the GeneSifter Data Center, an opportunity for any researcher to analyze high-quality, published data using the GeneSifter system for free; and MicroarraySuccess.com,for researchers new to microarrays. Free GeneSifter trial accounts are currently available.

View a pre-recorded product demo here.

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.

Demo | Support | Sales | Genomatix

ChipInspector is a microarray analysis and annotation software that works 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 you to group tiling probes with similar profiles. Direct links to Genomatix’ BiblioSphere PE, El Dorado 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 GeneChip-compatible webcast illustrating analysis of the Human Promoter Tiling Array data set with SP1 transcription factor.

CisGenome | Support | Download

CisGenome is an integrated tool for analyzing genome-wide chromatin immunoprecipitation data. The software provides a full spectrum of functionalities to support both upstream and downstream analysis of GeneChip Tiling Arrays. Using its graphical user interface, one can easily perform data exploration, array normalization, peak detection, gene annotation, sequence retrieval and motif analysis. The array, peak, gene structure, motif, cross-species conservation and genome sequence information can be visualized by the CisGenome Browser. The software runs on a PC. For computational biologists who wish to run batch jobs, it can also be used on most Unix platforms in a command-line manner. The software is free for academic users.

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek Genomics Suite (Partek GS) provides easy-to-use workflows for tiling experiments like 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 you can select regions of interest and create lists of genes, SNPs or sequences in those regions. Results are presented in an 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 an analysis of the Human Promoter Tiling Array data set with SP1 transcription factor.

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.

Expressionist | Support | Genedata

Genedata Expressionist® is a flexible, enterprise solution that manages, processes, analyzes, and visualizes omics data of unlimited size, including the complete transcriptome, genome, methylome, proteome, or metabolome. Its integrated mapping technology supports biological interpretation of the most complex data sets while facilitating decision making. Genedata Expressionist provides a single-point-of-access system for experimental, proprietary, and public data, including sample information, raw, and pre-processed data. Combining analysis results with reports and documentation, the system helps to bridge the gap between biology and statistics by making advanced statistical tools accessible to a wide range of users. Collaboration through session sharing and graphical analysis workflows gives interdisciplinary teams a platform on which to communicate, discuss, and interpret the results of biological experiments.

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek Genomics Suite (Partek GS) provides easy-to-use workflows for tiling experiments like 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 you can select regions of interest and create lists of genes, SNPs or sequences in those regions. Results are presented in an 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 an analysis of the Human Promoter Tiling Array data set with SP1 transcription factor.

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.

PathwayStudio | Technical Specifications | Support | Demo | Sales | Ariadne Genomics

PathwayStudio (formerly known as PathwayAssist) helps you to interpret microarray data in the context of pathways, as well as construct regulatory networks and protein-protein interaction maps. The software can classify and prioritize proteins; analyze pathways; export, import and filter data; and automatically update pathways with newly published information.

With PathwayStudio you can:

  • Identify relationships among proteins, small molecules, cell processes and treatments
  • Reconstruct pathways from microarray and other experimental data
  • Automatically extract biological interactions from scientific literature

PathwayStudio comes with a proprietary ResNet database of functional relationships between proteins, genes, cell objects, drugs and diseases automatically extracted from scientific literature. ResNet includes more than 1,000 reconstructed pathways, and more than 1 million relationships (the complete collection is supplied with the client-server version). The software also works with leading public and commercial databases of signaling and biochemical pathways, including KEGG, BIND, GO, STKE Connections Maps and Prolexys HyNet™.

View Ariadne’s recent GeneChip-compatible™ Webtalk

ExPlain Analysis System | TRANSFAC® | Support | Sales | BIOBASE

The ExPlain Analysis System applies a new knowledge-driven approach to the analysis of whole complexes of co-expressed genes. The internal Composite Module Analyst (CMA) is a genetic algorithm for the analysis and prediction of relevant promoters in the identified set of given genes obtained for sources such as GeneChip arrays. This combinatorial analysis drops false positive rates significantly and enables scientists to find potential causes for specific cellular events.

The power of correct prediction in ExPlain is driven by TRANSFAC®, a knowledge base of high-quality, expert-level and manually curated published scientific literature. TRANSFAC presents data on transcription factors, their experimentally-proven binding sites and regulated genes.

Sales | GeneGo

MetaCore enables life science researchers to analyze microarrays, SAGE, proteomics, metabolomics and phenotypic experimental data in the context of biological mechanisms. The platform is based on the most comprehensive up-to-date and expert-curated database of “small experiments,”, mammalian protein interactions, enzymatic reactions and bioactive molecules (drugs, metabolites and toxins). This includes millions of data points. The content includes the largest collection of unique maps with thousands of signaling, regulation and metabolic pathways established for human. GeneGo’s customers are empowered by an intuitive analytical toolkit for data import, visualization and exchange with eight unique networking algorithms, multiple specificity filters and a networks comparison module. MetaCore is available online and as a stand-alone server for in-house installations.

Demo | Support | Sales | Genomatix

BiblioSphere Pathway Edition is a dynamic data-driven gene network construction and analysis based on Genomatix Knowledge Base Ontology, literature and sequence analysis. BiblioSphere PE automatically creates the entire network of biological connections between input and correlated genes. User are supported by various tools to facilitate focusing on functional sub-nets and assisted in finding the most relevant biological context. There is no size limit for networks to be analyzed and integration of sequence analysis provides additional independent lines of evidence. This is achieved by applying Genomatix’ proprietary genome annotation and its unique promoter and transcription factor binding site database.

IPA | Technical Specs | Support | Sales | Demo | Ingenuity Systems

With Ingenuity Pathway Analysis (IPA), scientists can simultaneously analyze multiple genomic and proteomic datasets to rapidly gain biological insight and understanding. Scientists are using this innovative technology to make better and faster decisions in all areas of drug discovery and development, from target identification and validation to biomarkers, predictive toxicology and patient stratification. The application makes use of the Ingenuity Pathways Knowledge Base, the world’s largest curated database, which consists of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs and diseases. IPA is available as a web-delivered, hosted or deployed solution.

View Ingenuity Systems’ GeneChip-compatible™ Webtalk.

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.

Geneus | Demo | GenoLogics

Geneus completely interconnects your lab, including science, instruments, technologies and software. It is a robust solution that streamlines lab operations.

Geneus is a laboratory information management system (LIMS) designed for genomics centers conducting gene expression or genotyping. Unlike traditional generic LIMS products, Geneus is built specifically for genomics applications, enabling users to capture, integrate, store and access data from gene expression and genotyping experiments. The system is configurable and can adapt to rapidly changing needs and new lab technologies. It can be implemented and configured in days across multiple labs, and can be configured by the user or by GenoLogics’ service professionals to accommodate additional sciences and applications. Geneus is a reliable commercial lab and data management solution that will streamline your operations today and in the future.

View a webinar that briefly demonstrates the seamless, automated integration between Geneus and the GeneChip Operating System (GCOS) and Affymetrix GeneChip Command Console (AGCC).

 

Ocimum Biosolutions

The Biotracker™ laboratory information management system (LIMS) is a multi-platform, multi-user, cost-effective tool designed to improve laboratory performance. It enables life science research and development personnel to accurately track samples/specimens, reagents, instruments, workflow processes, and output. Researchers can easily keep track of their experimental design during various stages of the research process. The Biotracker system is compliant with GLP, HL7, HIPAA, and US FDA 21 CFR Part 11.

The specialized genomics modules (gene expression, genotyping, and sequencing) help users gather, validate, manage, store, retrieve, report, and analyze the vast amount of genomic data generated in low-, medium-, and high-throughput gene expression, genotyping, and sequencing studies while keeping pace with regulatory compliance.

The Biotracker LIMS is compatible with the Affymetrix GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC) and supports sample tracking, reagent inventory, and process flow challenges involved in microarray experiments.

Sales | GeneGo

MetaCore enables life science researchers to analyze microarrays, SAGE, proteomics, metabolomics and phenotypic experimental data in the context of biological mechanisms. The platform is based on the most comprehensive up-to-date and expert-curated database of “small experiments,”, mammalian protein interactions, enzymatic reactions and bioactive molecules (drugs, metabolites and toxins). This includes millions of data points. The content includes the largest collection of unique maps with thousands of signaling, regulation and metabolic pathways established for human. GeneGo’s customers are empowered by an intuitive analytical toolkit for data import, visualization and exchange with eight unique networking algorithms, multiple specificity filters and a networks comparison module. MetaCore is available online and as a stand-alone server for in-house installations.

Home | Support | Contact Us

Stone Bond Technologies is a leader in automated laboratory information management systems (LIMS), providing software solutions that help healthcare, pharmaceutical and biotech research facilities improve the quality of their research data while reducing their administration costs. EE-LIMS is based on the power of Stone Bond's Enterprise Enabler. EE-LIMS can rapidly improve services across shared lab facilities while eliminating costs normally associated with traditional paper processes and repetitive data manipulation. EE-LIMS enables researchers to manage massive amounts of data through labs quickly and more cost-effectively. Researchers gain the ability to query, analyze and manage information easily from the initial request for services all the way through to results, billing, research, reporting and discovery.

View a recent GeneChip-compatible webcast illustrating the integration of GeneChip® Operating System (GCOS) and Affymetrix GeneChip Command Console (AGCC) sample registration with Stone Bond’s Enterprise Enabler and EE-LIMS.