Agilent GeneSpring GX data analysis

GeneSpring GX from Agilent Technologies provides statistical tools for fast visualisation and analysis of expression and genomic structural variation data.

It offers an interactive desktop computing environment, is developed on avadis from Strand Life Sciences and is part of Agilent’s GeneSpring Analysis Platform for systems-level research.

Its features include: application for genomic copy number analysis - identify genomic copy number variant regions, LOH, allele-specific copy number variations and common variations across a set of samples; application for genome-wide association analysis - identify SNPs or haplotypes with significant association to an observable trait; analyse transcriptomics data to detect alternative splicing events, identify differentially expressed genes and microRNAs; uncover interesting patterns in data using principal component analysis, clustering methods and powerful class prediction algorithms; extend functionality using JYTHON application programming interface and fully integrated R programming language; display and overlay annotations and data from different experiment types, eg, gene expression, genomic copy number and genotyping in a genome browser; place statistically significant results into a biological context using GO analysis, gene set enrichment analysis, gene set analysis and pathway analysis; build biological networks to model interactions of identified genes of interest using provided species-specific pathway interaction databases; manage, store and analyse multi-omics data in a scalable workgroup.