Partek Genomics Suite

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract Partek Genomics Suite (Partek GS) is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. Designed for high-dimensional genomic studies containing thousands of samples, Partek GS is advanced, 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. Product is Affymetrix GeneChip-compatible for gene expression, exon, chromosomal copy number analysis, tiling and SNP analysis, and can import data from .CEL, .CHP, .CNT (CNAT), and plain text file formats, while automatically providing links to NetAffx, UCSC Genome Browser, IGB, and other internet databases. With Partek GS, you can import and analyze gene expression or other genomic data, reliably identify and annotate the genes or biomarkers of interest, and share findings with other researchers in your organization with information rich graphical displays.

Optimized for Affymetrix Technologies -

Product integrates advanced statistics and interactive visualization to extract meaningful patterns that are hiding in your data. It can import and analyze raw and processed data from all major Affymetrix GeneChip technologies, including gene expression arrays, exon arrays, 10K, 100K, and 500K mapping arrays, SNP 5.0 and SNP 6.0 arrays, and promoter and full tiling arrays.

Partek GS consists of 1) Partek GS for Gene Expression Data, 2) Partek GS for Exon Data, 3) Partek GS for Copy Number Data, 4) Partek GS for Promoter Tiling Data, and 5) Partek GS for SNP Association Studies.

1) Partek GS for Gene Expression Data -

a) Offers the ability to quickly and reliably identify patterns in your genomic data - Biological signals in genomic data is often hidden in a sea of noise. Biological factors such as dose, time, and phenotype combine with technical factors such as sample processing batches, and often obscure the important signals the biology is sending. The ability to draw reliable conclusions from today’s genomic studies requires that major factors influencing the data be identified and undesired effects removed revealing the true biological signals. With Partek GS, biologists, bioinformaticists, and statisticians have a single, integrated solution to the genomics data analysis bottleneck that produces trustworthy results.

2) Partek GS for Exon Data -

a) Detect Gene-Level, Exon-Level, and Alternative Splice Expression Patterns - It provides rigorous and easy-to-use statistical tests for differential expression of genes or exons, and a flexible and advanced statistical test to detect alternative splicing based on a mixed model analysis of variance. In addition, the Partek Genome Browser can display exon-level events such as alternative splicing and differential expression.

b) Build & Validate Diagnostic & Prognostic Classifiers - The Automated Model Selection tool in Partek GS will find an optimal set of predictive genes or exons, the best classifier, and optimal tuning parameters to obtain the best prediction possible from your data.

c) Import & Normalization of High Density GeneChip Exon Arrays - The Affymetrix Exon array provides incredible detail about the genomic expression of a sample, with more than 5 million probes and more than 1 million exons per array! Since simple pre-filtering to exclude low expressed probes or exons may ignore alternative splicing, product has been optimized to process and analyze all exons on the array at the probe level, exon level, or gene level.

3) Partek GS for Copy Number Data -

a) Identify Regions of Chromosomal Amplification/Deletion & LOH using Robust Statistical Methods - Products statistical and visual features offer the ability to detect, display, and report on regions of amplification or deletions on the genome. In addition, regions of interest that differ between drug responders and non-responders can be identified using proven statistical methods.

b) Build & Validate Diagnostic & Prognostic Classifiers - The Automated Model Selection tool in this product will find an optimal set of predictive genes, SNPs, or exons, the best classifier, and optimal tuning parameters to obtain the best prediction possible from your data. Using Partek’s Model Selection Tool, you can build accurate diagnostic or prognostic prediction models based on copy number, LOH, or raw SNP expression values.

4) Partek GS for Promoter Tiling Data -

a) Identify Protein/DNA Binding Sites from ChIP on Chip Studies using Robust Statistical Methods - Partek GS statistical and visual features offer the ability to detect, display, and report on mapping sites of protein/DNA interaction in ChIP on Chip experiments. Seamlessly import from .CEL files, normalize to baselines samples, statistically detect regions of binding, map regions to genes, SNPs or sequences, and visualize genomic location of features.

b) Import All Probes from the Promoter Tiling Array - Product can import all 4.6 million probes from the Human Promoter Tiling Array allowing you to analyze the data in full and Not in batches, eliminating potential errors and wasted time.

5) Partek GS for SNP Association Studies -

a) Identify SNPs of Interest in Genotyping Data using Robust Statistical Methods - It supports single/multiple SNP association tests performed on allele, genotype, and dominant/recessive models. Confidently analyze your genotyping data using such statistical tests as Chi2, Hardy-Weinberg Equilibrium, and Linkage Disequilibrium. Receive 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.

System Requirements

Supported Operating Systems

Windows - Vista/XP/2000, Red Hat Linux - 7.x/9.x/EL3, Macintosh - coming soon!

Minimum System Requirements

256 MB RAM, 120 MB free disk space, 16-bit color, 1024x768 screen resolution, 1 GHz CPU

Manufacturer

Manufacturer Web Site Partek Incorporated

Price Contact manufacturer.

G6G Abstract Number 20023

G6G Manufacturer Number 102061