Partek Tutorial and Data Repository

The Partek Tutorial and Data Repository provides tutorials and data sets for analysis in Partek. Partek tutorials use specific data sets to show how to do data analysis and visualization. For the greatest learning benefit, they are designed to be used with their corresponding, provided data set. User Guides do not have a specific data set associated with them and are useful for learning general information. Note: The tutorials, user guides, and data sets in this section require Partek^® Genomics Suite^TM. If you have any questions contact Partek support.

Affymetrix

Down Syndrome Study
- Tutorial: Learn how to analyze a disease vs. normal study across multiple tissues with a focus on ANOVA contrasts and interactions (January 2009)
- Data [56M]
- CHP Files [3.3M]

Breast Cancer Study
- Tutorial: Learn how to analyze a time/dose experimental design with a batch effect (August 2009)
- Data [6M]

Agilent

Importing Data from Agilent's Feature Extraction Software
- User Guide: Learn how to import Agilent gene expression and copy number data into Partek (December 2008)

Illumina

Gene Expression Analysis of an Age Study Using Illumina Microarray Technology
- Tutorial: Learn how about comparing the performance of different ANOVA analysis and the impact on both genes and biological intepretation using Illumina microarray technology (June 2009)
- Data [6.2MB]

GenomeStudio

Importing Gene Expression Data from GenomeStudio
- User Guide: Learn how to export gene expression data from GenomeStudio into Partek GS by using the Partek Gene Expression Plug-in (April 2009)
- The Partek Gene Expression Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Final Report Text File

Importing the Final Report from GenomeStudio for Gene Expression Data
- User Guide: Learn how to import the Final Report from GenomeStudio into Partek GS (April 2008)

NimbleGen

Importing NimbleGen Data
- User Guide: Learn how to import NimbleGen gene expression data into Partek (December 2008)

Survival Analysis

GSE3494 p53 Status in Breast Cancer
- Data [31M]
- Sample Information [8K]
- CEL Files [external link]

Next-Gen Sequencing

Illumina
ChIP-seq

Find IP Regions and Motifs Using ChIP-seq
- Tutorial: Learn how to find IP regions and motifs within a ChIP-seq data set (June 2010)
- Data [70MB]

RNA-seq

Analysis of RNA-Seq data within Partek GS using the RNA-Seq Workflow (June 2010)
- Tutorial: Learn how to use the RNA-seq workflow within Partek GS to import, analyze, and visualize RNA-Seq data
- Data [2.3GB]

SNP

Analysis of Nucleotide Variations within Partek GS (March 2010)
- Tutorial: Learn how to detect nucleotide differences and annotate SNP calls with overlapping genes
- Data

FAQ

Frequently Asked Questions for Next Generation Sequencing in Partek GS (March 2010)
- FAQ: Find answers to some of the common next generation sequencing questions regarding Partek GS

Web Talks:

Applied Biosystems Web Talk: Analysis of SOLiD™System RNA-Seq Data in Partek Genomics^® Suite™ (September 15, 2009)
Illumina Web Talk: Analysis of Illumina mRNA-Seq Data in Partek Genomics^® Suite^TM (May 27, 2009)

Exon

Colon Cancer Study: Learn how to analyze a paired experimental design, cancer vs. normal
- Import Tutorial: Learn how to import CEL files into Partek (December 2007)
- Alternative Splicing Analysis Tutorial: Learn how to define alternatively spliced genes in a data set (September 2008)
- Gene-level Analysis Tutorial: Learn how to discover differentially expressed genes between colon cancer vs. normal (September 2007)
- CEL Files and Sample Information [372M]
- Colon Cancer Data and Images [266M]

Web Talks:

Partek Genomics Suite for the Analysis of GeneChip Exon Arrays (February 2008) [Windows only - Note: this is a downloadable wrf file (Webex Record File). To view the file, you can download the free player from WebEx.]

Partek Video Information Series:

Differential Gene Expression and Alternative Splice Analysis of Affymetrix Exon GeneChips using Partek Genomics Suite (February 2008) [6 minutes]
- Streaming Video [no download necessary]
- Windows Media File [download - 6MB]
- QuickTime File [download - 143MB]

microRNA

Analyzing microRNA Data & Integrating microRNA with Gene Expression Data in Partek
- Tutorial: Learn how to analyze microRNA data within Partek, as well as how to integrate microRNA data with gene expression data in Partek (April 2009)
- Data [370K]

Copy Number

General Copy Number Topics

Optimizing Copy Number Segmentation in Partek
- Tutorial: Learn how to find regions of copy number variation using Genomic Segmentation (April 2009)
- Data [168M] (paired tumor/normal samples)

Affymetrix
SNP 6

Overlapping Copy Number with LOH
- Copy Number and LOH Data: Learn how to integrate copy number and LOH data within Partek GS (May 2009)
- Data [294M]
Copy Number Analysis in Partek GS v6.4 with FFPE Samples
- User Guide: Learn the latest Copy Number workflows in Partek GS v6.4. Optional restriction fragment-length filters are shown to enhance performance on FFPE samples on SNP6 arrays (July 2008)
HapMap Sample: Learn how to do copy number analysis within a normal population
- Copy Number (December 2007)
- Allele Ratio (August 2007)
- Data [581M] (20 HapMap samples)
Allele Specific Copy Number Analysis with Cancer Sample
- Tutorial: Learn how to analyze Allele Specific copy number (best used for primary tumor heterogeneous samples with possible normal contamination) (December 2007)
- Data [168M] (paired tumor/normal samples)

Mapping 500K

ATCC Carcinoma Study (Mapping 500K)
- Analysis Tutorial: Learn how to analyze Mapping 500K data (December 2007)
- Paired Import Tutorial: Learn how to import a paired sample data set into Partek (December 2007)
- Unpaired Import Tutorial: Learn how to import an unpaired sample data set into Partek (December 2007)
- Data [870M]
- Copy Number Baseline [9.3M]

Mapping 100K

NCI60 Cell Line Study
- CNAT Import Tutorial: Learn how to import CNAT data (December 2007)
- Visualization Tutorial: Learn how to visualize CNAT data (April 2007)
- Analysis with U95 Gene Expression: Learn how to integrate 100K Copy Number Data with Exon Data (December 2007)
- Analysis with Exon Expression: Learn how to integrate 100K Copy Number Data with Gene Expression Data (December 2007)
- Data [508M]
- CEL Files [1.7G]

Agilent

Importing Data from Agilent's Feature Extraction Software
- User Guide: Learn how to import Agilent gene expression and copy number data into Partek (December 2008)

CNAG

Importing from CNAG
- User Guide: Learn steps for importing data from CNAG into Partek (December 2007)

dChip

Importing from dChip
- User Guide: Learn steps for importing data from dChip into Partek (December 2007)

Illumina

GenomeStudio

Importing Genotyping Data from GenomeStudio
- User Guide: Learn how to export genotyping data from GenomeStudio into Partek GS by using the Partek Genotype Plug-in (April 2009)
- The Partek Genotype Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Final Report Text File

Analyzing Illumina Copy Number Data in Partek
- Tutorial: Learn how to import GenomeStudio data into Partek, generate paired copy number, identify regions of copy number, and generate a list of genes in a region (November 2008)

NimbleGen

Importing NimbleGen Data
- User Guide: Learn how to import NimbleGen copy number data into Partek (December 2008)

Web Talks:

Copy Number & LOH of Cancer Samples on the Human SNP Array 6.0 Using Partek GS (October 2007)
- Windows Media File [download - 58MB]
Identifying Copy Number Variation using the Affymetrix SNP Array 6.0 and Partek (June 2007)
- Windows Media File [download - 58MB]
- PowerPoint (in PDF) [download - 17MB]

Partek Video Information Series:

Exporting from GenomeStudio's Genotyping Module and Analyzing Copy Number Data in Partek Genomics Suite (February 2008) [4 minutes]
- Streaming Video [no download necessary]
- Windows Media File [download - 4MB]
- QuickTime File [download - 129MB]
Copy Number Analysis Using Partek GS (August 2008) [6 minutes]
- Streaming Video [no download necessary]
- Windows Media File [download - 40MB]
- QuickTime File [download - 177MB]

Integrated Genomics

Colon Cancer Study: Exon
- Gene-Level Analysis: Learn how to integrate exon data with Gene Expression Data (September 2007)
NCI60 Cell Line Study: Copy Number
- Analysis with U95 Gene Expression: Learn how to integrate 100K Copy Number Data with Gene Expression Data (December 2007)
- Analysis with Exon Expression: Learn how to integrate 100K Copy Number Data with Exon Data (December 2007)
Integrating and Correlating Gene Expression and Copy Number
- Expression and Copy Number: Learn how to integrate gene expression and copy number data within Partek GS (January 2009)
- Data [19M]
Overlapping Copy Number with LOH
- Copy Number and LOH Data: Learn how to integrate copy number and LOH data within Partek GS (May 2009)
- Data [294M]

Partek Video Information Series:

Extending & Enhancing Expression Analysis through Integration with Genome-wide Assays (December 2008) [5 minutes]
- Streaming Video [no download necessary]

Regulation Using Tiling Microarrays or Next-Gen Sequencing

Affymetrix
ChIP-chip

Finding IP Regions Using ChIP-chip and Integrating Regulation and Gene Expression Data
- Tutorial: Learn how to analyze and integrate regulation and gene expression data within the same study (February 2009)
- Data [84M]

Illumina
ChIP-seq

Finding IP Regions and Motifs Using ChIP-seq
- Tutorial: Learn how to find IP regions and motifs within a ChIP-seq data set (April 2009)
- Data [70MB]

GenomeStudio

Importing Methylation Data from GenomeStudio
- User Guide: Learn how to export methylation data from GenomeStudio into Partek GS by using the Partek Methylation Plug-in (March 2010)
- The Partek Methylation Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Partek Express

Frequently Asked Questions

Affymetrix

Analyzing Affymetrix Data in Partek Express
- Tutorial: Learn how to analyze a disease vs. normal study in Partek Express (May 2010)
- Data

Agilent

Analyzing Agilent Data in Partek Express
- Tutorial: Learn how to import Agilent gene expression and copy number data into Partek (May 2010)
- Data

Illumina

Analyzing Illumina Data in Partek Express
- Tutorial: Learn about gene expression analysis of an age study Using Illumina Microarray Technology (May 2010)
- Data

NimbleGen

Analyzing NimbleGen Data in Partek Express
- Tutorial: Learn how to import NimbleGen gene expression data into Partek Express (May 2010)
- Data

Frequently Asked Questions

Frequently Asked Questions
- FAQ (May 2010)

User Guides

Model Selection
- User Guide: Understanding the Model Selection tool in Partek GS (April 2010)

Chromosome Viewer
- User Guide: Understanding the Chromosome Viewer in Partek GS (March 2010)

Hierarchical Clustering
- User Guide: Hierarchical Clustering Analysis of Microarray Data (January 2009)

Adding Annotations
- User Guide: Learn how to associate a spreadsheet with an annotation file. Note: adding annotations is required if importing genomic data as a text (.txt) file (November 2010)

Creating a Sample Information File
- User Guide: Learn steps to create your own sample information file, useful when importing large data sets (June 2008)

Displaying Genes from UCSC Annotation Files
- User Guide: Learn how to display genes using a UCSC gene annotation file (June 2008)

Using .bed Files in Partek to Output Data
- User Guide: Learn how to prepare a .bed file in Partek GS to output for upload to genome browsers, such as the UCSC Genome Browser (June 2008)

GO ANOVA
- User Guide: Learn about Partek's GO ANOVA (August 2009)

GO Enrichment
- Tutorial: Learn how to perform GO Enrichment analysis in Partek GS (March 2009)
- Data [16M]

Understanding the Affymetrix QC metrics options
- User Guide: Understand the many results and options of the QC metrics feature for Partek Genomics Suite and Partek Express (November 2010)

High-Throughput Screening Examples for use with Partek Screening Solution
Note: This tutorial and data set require Partek^® Screening Solution^TM.

Normalization and Hit-Selection of an HTS Campaign

384-Well Plate
- Tutorial: Learn how to analyze 384-well plate data (September 2007)
- Data [876K]

White Papers

RNA-Seq

Detecting Single Nucleotide Variations in Sequencing Data using Partek GS
- White Paper: Learn about the algorithm that Partek GS uses to detect SNP/SNV from next generation sequencing data (May 2010)

Understanding RNA-Seq Methods in Partek GS
- White Paper: Learn how Partek GS estimates expression levels of transcripts and quantifies alternative splicing of a gene (June 2010)

Copy Number

New Copy Number Processes in Partek Genomics Suite v6.5
- White Paper: Learn about new copy number features in Partek GS, version 6.5 (January 2010)

Understanding Allele Intensity Import
- White Paper: Learn how Partek GS imports Allele Intensity for Copy Number (January 2009)

Understanding Allele Specific Copy Number
- White Paper: Learn how Partek GS calculates Allele Specific Copy Number (September 2008)

Understanding Loss of Heterozygosity
- White Paper: Learn how Partek GS calculates Loss of Heterozygosity (June 2008)

Understanding Genomic Segmentation
- White Paper: Learn about the genomic segmentation algorithm in Partek GS (June 2008)

ChIP-Chip

Detecting Regions of Significance
- White Paper: Learn how Partek GS finds regions of binding in ChIP-Chip studies (December 2008)

ChIP-Seq

Fragment Length Analysis
- White Paper: Learn how Partek GS estimates average fragment length in ChIP-Seq data (December 2010)

Detecting ChIP-Seq Peaks
- White Paper: Learn how Partek GS detects peaks in ChIP-Seq studies (June 2010)

Motif Discovery
- White Paper: Learn about the methods Partek GS uses to search for motifs in a set of genomic regions (April 2010)

Forum Series

Submit forum questions to Partek Workshops.

Past Forums

Biological Interpretation

Biological Interpretation
February 9, 2010

Partek Biological Intepretation Web Forum: Biological Interpretation in Partek Genomics Suite This will include the use and understanding of gene ontology enrichment and GO ANOVA tools in Partek.
- Windows Media File [download - 38MB]
- PowerPoint [download - 2MB]

June 18, 2009

Partek Biological Intepretation Web Forum: using Partek to analyze gene expression data for biologically relevant changes. This will include the use and understanding of gene ontology enrichment and GO ANOVA tools in Partek.
- Windows Media File [download - 103MB]
- PowerPoint [download - 745KB]

Copy Number
December 3, 2009

Analyzing Copy Number in Partek Genomics Suite
- Windows Media File [download - 68MB]
- PowerPoint [download - 2MB]

July 21, 2009

Introduction to LOH and Allele Specific Copy Number Web Forum: presents the use of Partek to analyze SNP array data for allele specific aberrations
- Windows Media File [download - 86MB]
- PowerPoint [download - 680KB]

July 14, 2009

Intro to Copy Number Web Forum: understand how to use Partek to analyze copy number and CGH data for copy number variants
- Windows Media File [download - 86MB]
- PowerPoint [download - 2MB]

May 14, 2009

Partek Segmentation Web Forum: the application and optimization of Partek's recommended segmentation algorithm for copy number and CGH analysis
- Windows Media File [download - 80MB]
- PowerPoint [download - 422KB]

Exon
June 11, 2009

Partek Exon Web Forum: using Partek to analyze exon and whole transcript arrays with a focus on finding genes undergoing potential alternate splicing and differential transcript expression
- Windows Media File [download - 103MB]
- PowerPoint [download - 448KB]

Gene Expression
March 4, 2010

Partek Gene Expression Web Forum: The Gene Expression Workflow in Partek GS
- Windows Media File [download - 110MB]
- PowerPoint [download - 1MB]

May 28, 2009

Partek Gene Expression Web Forum: using the Gene Expression Workflow within Partek
- Windows Media File [download - 104MB]
- PowerPoint [download - 1MB]

Integrated Genomics
November 19, 2009

Reap the Benefits of Publicly Available Data - Integrated Genomics at Your Fingertips
- Windows Media File [download - 47MB]
- PowerPoint [download - 1MB]

November 12, 2009

See the Larger Picture: Integrate Gene Expression and Copy Number, with a Workflow
- Windows Media File [download - 56MB]
- PowerPoint [download - 1MB]

microRNA
October 29, 2009

Focus on microRNA: The Data Analysis Workflow
- Windows Media File [download - 103MB]
- PowerPoint [download - 4MB]

Next-Generation Sequencing
December 09, 2010

Statistical Tools for Next Generation Sequencing Data Analysis
- Windows Media File [download - 93MB]

October 07, 2010

Whole Transcriptome Analysis of Illumina RNA Seq Data
- Windows Media File [download - 73MB]
- PowerPoint [download - 9.7MB]

May 11, 2010

Integration of Next Generation Data in Partek® Genomics Suite™
- Windows Media File [download - 107MB]

March 25, 2010

Interpretation of Next Generation Data in Partek® Genomics Suite™
- Windows Media File [download - 58MB]
- PowerPoint [download - 3MB]

December 16, 2009

Next Generation Sequencing Data Analysis in Partek® Genomics Suite™
- Windows Media File [download - 50MB]
- PowerPoint [download - 3.6MB]

November 5, 2009

Focus on RNA-Seq: The Data Analysis Workflow
- Windows Media File [download - 46MB]
- PowerPoint [download - 3.3MB]

September 3, 2009

RNA-Seq: Next Generation RNA Analysis Web Forum: explores the use of Partek to analyze next generation RNA expression data
- Windows Media File [download - 73MB]
- PowerPoint [download - 780KB]

July 28, 2009

ChIP-Seq: Next Generation ChIP Analysis Web Forum: presents the use of Partek to analyze next generation chromatin immuno-precipitation data
- Windows Media File [download - 64MB]
- PowerPoint [download - 616KB]

Regulation
May 4, 2009

Partek ChIP-Chip Web Forum: the application of whole genome arrays for peak detection
- Windows Media File [download - 84MB]
- PowerPoint [download - 27KB]

Statistics
November 18, 2010

Partek Statistics Web Forum: Clinical Applications & Microarray Data Analysis
- Windows Media File [download - 40MB]
- PowerPoint [download - 4.6MB]

October 26, 2010

Partek Statistics Web Forum: Statistical Concepts Laying the Foundation for Microarray and NGS Data Analysis
- Windows Media File [download - 82MB]
- Q and A Session MP4 [download - 12MB]
- PowerPoint [download - 5.6MB]

June 22, 2010

Partek Statistics Web Forum: Statistical Analysis for Microarray and Next-Generation Sequencing Studies
- Windows Media File [download - 108MB]
- PowerPoint [download - 2.5MB]

January 21, 2010

Partek Statistics Web Forum: Experimental Design & Statistical Analysis for Microarray and Next-Generation Sequencing Studies
- Windows Media File [download - 69MB]
- PowerPoint [download - 2MB]

Partek Express
June 02, 2010

Partek Express Web Forum: The Most User-Friendly Gene Expression Microarray Analysis Software
- Windows Media File [download - 53MB]
- PowerPoint [download - 2MB]

Frequently Asked Questions

FAQ: Find answers to some of the common questions regarding Partek GS (January 2011)

Partek Distributed Copy Number and Baseline Files

Affymetrix

Illumina

Affymetrix
Partek GS v6.5

*Note: The baseline files generated and used in Partek 6.5 are not compatible with Partek 6.4 and earlier.

Genome Wide SNP 6
270 GenomeWide SNP 6.0 HapMap Samples

Copy Number Baseline: Partek generated baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [55M]
Sample Information: Partek generated sample information file containing 270 samples [8K]
LOH Baseline: Partek generated LOH baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [3.8M]

794 GenomeWide SNP 6.0 HapMap Samples

Copy Number Baseline: Partek generated baseline from the 794 GenomeWide SNP 6.0 HapMap samples available from the International HapMap Project website [54M]
Sample Information: Partek generated sample information file containing 794 samples [8K]

Genome Wide SNP 5

Copy Number Baseline: Partek generated baseline from the 44 GenomeWide SNP 5.0 HapMap samples available from Affymetrix [5M]

Mapping 500K

Copy Number Baseline: Partek generated baseline from the 270 Mapping 500K Nsp/Sty HapMap samples available from GEO [21M]

Mapping 100K

Copy Number Baseline: Partek generated baseline from the 90 Mapping 100K Hind/Xba HapMap trio samples available from Affymetrix [4.7M]

Partek GS v6.4
Genome Wide SNP 6

Library Files: Includes Chromosome Variation, Chip Sequence Summary, and Fragment Length Summary files [44M]
Copy Number Baseline: Partek generated baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [12M]
Allele Ratio Baseline: Partek generated allele ratio baseline from the 270 GenomeWide SNP 6.0 HapMap samples [18M]
LOH Baseline: Partek generated LOH baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [3.8M]

Genome Wide SNP 5

Library Files: Includes Chromosome Variation, Chip Sequence Summary, and Fragment Length Summary files [34M]
Copy Number Baseline: Partek generated baseline from the 44 GenomeWide SNP 5.0 HapMap samples available from Affymetrix [5M]
Allele Ratio Baseline: Partek generated allele ratio baseline from the 44 GenomeWide SNP 5.0 HapMap samples [4.9M]

Mapping 500K

Copy Number Baseline: Partek generated baseline from the 270 Mapping 500K Nsp/Sty HapMap samples available from GEO [3M]
Allele Ratio Baseline: Partek generated allele ratio baseline from the 270 Mapping 500K Nsp/Sty HapMap samples [9.3M]

Mapping 100K

Copy Number Baseline: Partek generated baseline from the 90 Mapping 100K Hind/Xba HapMap trio samples available from Affymetrix [680K]

Illumina
Partek GS v6.5*

*Note: The baseline files generated and used in Partek 6.5 are not compatible with Partek 6.4 and earlier.

Illumina Human 1M

Copy Number Baseline: Partek generated baseline from 125 Human1M HapMap samples [40M]

Illumina Human Omni1-Quad

Copy Number Baseline: Partek generated baseline from 167 Human Omni1-Quad Hapmap Samples (43M)
Sample Information: Partek generated sample information file containing 167 samples (4K)

Partek GS v6.4
Illumina Human 1M

Copy Number Baseline: Partek generated baseline from 125 Human1M HapMap samples [6.8M]