GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context. Multi-omic analysis with Agilent’s GeneSpring 11.5 bioinformatics Integrative platform for multi-omic data analysis Transcriptomic analysis Genomic copy number analysis Genome-wide association analysis Proteomic and metabolomic analysis Built-in ID browser automates database and spectral library searches Comprehensive analytical and visualization toolkit Statistical tools for testing differential expression Pattern discovery Extensible functionality with Jython and R Intuitive graphical displays Integrated toolbox for pathway analysis and biological contextualization Scalable architecture GeneSpring Licenses GeneSpring provides powerful, accessible statistical tools for fast visualization and analysis of microarray data. Designed specifically for the needs of biologists, GeneSpring offers an interactive computing environment that promotes investigation and enables understanding of microarray data within a biological context. Regarded as the gold standard in expression analysis, GeneSpring allows you to quickly and reliably identify targets of interest that are both statistically and biologically meaningful. GeneSpring has over 9,500 references in Google Scholar, including over 1,600 in peer reviewed publications. Developed on avadisTM from Strand Life Sciences, GeneSpring GX is part of Agilent’s GeneSpring Analysis Platform, an expanding suite of integrated software applications for systems-level research. Multi-omic analysis with Agilent’s GeneSpring 11.5 bioinformatics solution A key component of systems biology research involves producing heterogeneous,data that measure various biological entities and events such as DNA structural variation, mRNA and microRNA expression, exon splicing, proteins and metabolites. GeneSpring 11.5, a part of Agilent’s GeneSpring Analysis Platform, allows researchers to perform integrated analysis of such heterogeneous data, enabling them to identify linkages and data concordance that contribute to a more comprehensive understanding of the underlying mechanism of disease. Integrative platform for multi-omic data analysis GeneSpring 11.5 addresses the challenges in multi-omic data analysis by providing comprehensive analytical and visualization tools for multiple data types within a single data analysis application. With this platform, heterogeneous data such as gene expression, miRNA, exon splicing, genomic copy number, genotyping, proteins, and metabolites, can be combined into one project, allowing researchers to analyze, compare, and view results from different experiments in a single user interface (Figure 1). GeneSpring 11.5 facilitates integrative analysis through its translation function, linking probes across data types, array platforms, and organisms that map to the same biological entity. By supporting analysis and translation of multiple data types in a single application, GeneSpring 11.5 avoids common issues of software interoperability and faulty semantic mapping to increase a researcher’s ability to find linkages between data types. Zoom Figure 1. Project-based data organization enables you to store data from related experiments in a single workspace, regardless of data type, array platform, or organism. Transcriptomic analysis GeneSpring 11.5 provides flexible and comprehensive workflows for a variety of transcriptomic applications. Specifically, several new features that leverage the new exon-level content of Agilent’s Exon Microarrays have been implemented, including a new workflow, statistical routines, and a host of enhanced visualizations (Figure 2). A broad spectrum of data pre-processing, linear and non-linear normalization methods is available for both one- and two-color gene expression data. Depending on the researcher’s level of expertise, data analysis can be performed using either the Guided Workflow or Advanced Analysis mode. Quality control can be performed using platform-specific metrics, enabling researchers to optimize pre-processing steps before statistical analysis. Other key features for transcriptomic applications include: Probe-or gene-level expression analysis on all major microarray platforms, including Agilent, Affymetrix, and Illumina microRNA analysis and identification of gene targets using integrated TargetScan information Exon splicing analysis using t-tests or multivariate splicing ANOVA and filtering for transcripts on splicing index Real-time PCR data analysis NCBI Gene Expression Omnibus Importer tool for expression datasets Zoom Figure 2. GeneSpring 11.5 incorporates a new workflow, statistical routines, and a host of enhanced visualizations specifically created for the analysis of Agilent Exon Microarray data. Genomic copy number analysis GeneSpring 11.5 also supports the interrogation of genomic structural variations and their implications in disease susceptibility and progression. Providing workflows for paired and unpaired analysis of Affymetrix and Illumina genotyping array data, GeneSpring 11.5 enables scientists to quickly detect regions of genomic copy number variation (CNV) and loss of heterozygosity (LOH). Once regions of interest are discovered, genes overlapping those regions can be identified and the biological impact of copy number variation can be assessed in downstream GO Analysis or pathway analysis. Features of the genomic copy number workflow include: Ability to create and use a custom reference in addition to packaged HapMap reference Batch effect correction method Circular Binary Segmentation Filters to identify copy-neutral LOH events and regions of allelic imbalance Abilty to identify common variations across a set of samples Genome-wide association analysis Genome-wide association studies (GWAS) utilize high-density genotyping microarrays to identify SNPs associated with qualitative or quantitative traits. GeneSpring 11.5 provides a comprehensive workflow for case-control GWAS using Affymetrix and Illumina genotyping microarray platforms. The flexible workflow supports case-control experimental designs, offering a suite of statistical tests applied under various genetic models, multiple testing correction, and correction methods for population stratification. After identifying genes harboring SNPs or haplotype blocks associated with trait, researchers can perform GO Analysis and pathway analysis to determine what biological process and pathways may be involved in the disease under study. Other key features for the genetic association workflow include: EIGENSTRAT and Genomic Control population stratification correction Tag SNP identification Haplotype inference and Haplotype Trend Regression Pearson’s Chi-Square, Fisher’s Exact, Cochran Armitage, and Chi-Square correlation Logistic and linear regression LD plot Zoom LD plot provides fine-grained representation of the LD blocks, which are colored according to the pair-wise correlation provided as D’ or R2 values. SNPs within regions of strong LD can be saved as entity lists for further analysis.