Partek
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    • Live Training Event Recordings
      • Bulk RNA-Seq Analysis Training
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    • Tutorials
      • Creating and Analyzing a Project
        • Creating a New Project
        • The Metadata Tab
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        • Project Management
        • Importing a GEO / ENA project
      • Bulk RNA-Seq
        • Importing the tutorial data set
        • Adding sample attributes
        • Running pre-alignment QA/QC
        • Trimming bases and filtering reads
        • Aligning to a reference genome
        • Running post-alignment QA/QC
        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
        • Data Processing
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      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
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        • Import 10x Genomics Xenium Analyzer output
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        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
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    • User Manual
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      • Data Viewer
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        • Chromosome View
          • Launching the Chromosome View
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        • Dot Plot
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        • List Generator (Venn Diagram)
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      • How to select the best single cell quality control thresholds
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      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
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    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
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      • Lists
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        • Import gene expression data
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        • Import data from Illumina GenomeStudio using Partek plug-in
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    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
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        • Creating gene lists from ANOVA results
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        • Importing the data set
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        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
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      • Differential Methylation Analysis
        • Import and normalize methylation data
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        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
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        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
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        • Open a zipped project
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      • RNA-Seq Analysis
        • Importing aligned reads
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      • Survival Analysis
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        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
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      • Allele Intensity Import
      • Allele-Specific Copy Number
      • Calculating Genotype Likelihoods
      • ChIP-Seq Peak Detection
      • Detect Regions of Significance
      • Genomic Segmentation
      • Loss of Heterozygosity Analysis
      • Motif Discovery Methods
      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
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  • Introduction
  • Filtering Lists
  • Selecting Lists for Venn Diagram
  • Venn Diagram
  • Additional Assistance
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  1. Partek Flow
  2. User Manual
  3. Visualizations

List Generator (Venn Diagram)

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Last updated 7 months ago

  • Introduction

  • Filtering Lists

  • Selecting Lists for Venn Diagram

  • Venn Diagram

Introduction

Partek Flow has a List generator function that allows you to investigate unique and common features between different lists within a project. These can be visualized in a Venn diagram consisting of up to five sets.

Filtering Lists

Feature lists can be generated by RNA-Seq tasks such as GSA and ANOVA. Filter your feature lists as needed. In the example below, three feature lists were generated by filtering the same multivariate GSA result on three different contrasts. Each filtered list appears as its own layer on the Analyses tab.

Figure 1. Project with multiple gene lists

Selecting Lists for Venn Diagram

Note that you must be a collaborator in the project to see the purple List Generator button.

Figure 2. List selector window

If the current project does not contain any feature lists, a message will appear.

Figure 3. Error message appears when no lists within a project

The List name field can be customized to provide specific information about the selected list and will also serve as the set's name on the Venn diagram. Hovering your mouse over a specific feature list highlights its node location on the task graph.

Figure 4. Selecting feature list highlights data node

Conversely, clicking a feature list data node highlights the feature list on the right panel.

Figure 5. Selecting the data node

Figure 6. The Select identifier dialog box

For your convenience, example entries for each possible identifier is displayed. Select the radio button of the identifier you would like to use for comparison. Note that the List generator only uses Identifiers to determine common features within a list. For feature lists generated by automated tasks like Cufflinks' novel transcript discovery function, keep in mind that these identifiers may not be referring to the same feature.

Venn Diagram

Once you have selected your lists, click the Display selection button to invoke the Venn diagram.

Figure 7. Venn diagram window

To save the current diagram displayed, click the Save image button. Images can be either in SVG or PNG format. You can also define the size and resolution you want the diagram to be. To maintain the fidelity of the colors in the Venn Diagram, we recommend downloading the image in PNG format. If a vector-based file format is required, you can also export the diagram in SVG format.

The Venn diagram is also interactive. Hovering over specific sections of the diagram highlight the feature list represented by that section. A tooltip also appears describing the number of elements in that section.

Figure 8. Highlighted Venn diagram

To download a list of identifiers belonging to a section, click on the section (a striped pattern will appear) and click the Download list button. Multiple sections can be selected to download a merged list of all corresponding identifiers. The Total features selected display updates the number of features selected as you select more sections.

Figure 9. Downloading list of sections selected within a Venn diagram

To change the lists displayed, click the Select lists button. This will bring up the List selector again.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

To invoke the Venn diagram, click the button. This brings up the list selector window. Select the data nodes you would like to include on the diagram using the check boxes.

Click on the icon to select the identifier that will be used to compare between the sets. The Select identifier dialog box will then appear.