Transcriptomics Gene List

Transcriptomics Gene List Overview

A Gene List in PATRIC is a custom user-created list of genes based on the transcriptomics datasets of interest. Each Gene List displays all of the genes present in selected datasets, their functions, and summaries of their expression levels in various samples or comparisons. A Gene List can be dynamically filtered based on the identifiers/functions, expression levels, or up/down regulation in one or more comparisons. Any subset of genes of interest can be downloaded along with the annotations and expression values as tab-delimited text or Excel file; or saved as a Workspace group for further analysis. A complementary Heatmap Viewer enables quick sorting or clustering of genes and comparisons; and visualization of genes that are similarly expressed across one or more comparison

Accessing/Creating a Transcriptomics Gene List

A Gene List may be accessed while under the Transcriptomics Tab (available on any Taxonomy or Genome level landing page) in the following ways:

  • Select one or more Experiment(s) from either the Experiments Tab or the Comparisons Tab and then utilize the Table Toolbar, located in the light blue row to:
    • Create a Gene List by clicking the Gene List button.
    • Save selected items to groups within your Workspace by clicking the Add Feature(s) button. Your Workspace also contains a Table Toolbar with a Gene List button, where you may access the Gene List for the groups you create in your Workspace at any time.
  • From the Experiments Tab, click on links within the rows to navigate to the corresponding Gene List (Genes).
  • From the Comparisons Tab, click on links within the rows to navigate to the corresponding Gene List (Genes), list significant genes based on log ratio (|Log Ratio| >= 1), or list significant genes based on Z-score (|Z-score| >=2).

Note: To learn more about how to save data for future visits and utilize your personal Workspace please see Workspace FAQs. To learn about Transcriptomics and Experiments and Comparisons Lists, see Transcriptomics Experiment and Comparison List FAQs.

Filtering a Gene List

Both the Table and Heatmap Tabs can be filtered using the filter panel on the left of the Gene List page in following ways:

  • Use the arrows to show genes that are up or down regulated in the subset of comparisons of interest.
  • Entering one or more keywords related to genome name, gene functions, or locus tags. Note: Separate multiple keywords/locus tags with a comma or a new line.
  • Based on the |Log Ratio| and/or |Z-score| cut-off of your choice.

Gene List Table Table Features and Functionality

  • Sort the Gene List table as described in Feature Table FAQs.
  • View the number of comparisons in which a gene is reported and up/down regulated. Click on the number to see the expression of the gene in those comparisons.
  • Use the Gene List Table Toolbar located in the light blue row to:
    • Save selected items to groups within your Workspace by clicking the Add Feature(s) button. To learn more about how to save data for future visits and utilize your personal Workspace see Workspace FAQs.
    • View or download selected DNA and/or protein sequence data in FASTA format. The Gene List tables themselves, or selected data within them, are also downloadable in both excel and txt file formats.
    • View pathways and associated pathway information for your selected genes by clicking the Pathway Summary button.
    • Conduct Multiple Sequence Alignment analysis on selected groups, or selected items within groups, by clicking the Multiple Sequence Alignment button. For more details on this tool please see Multiple Sequence Alignment FAQs.
    • Utilize the ID Mapping Tool on selected items by clicking the Map IDs button. For more information on this tool please see ID Mapping FAQs.
    • Customize columns shown/hidden in your results table with the Columns button.
  • Click on any Locus Tag link within a row to visit the corresponding Gene landing page. From here you may:
    • View information about the functional properties of the gene.
    • Click on the Transcriptomics Tab to view expression of that gene across all available experimental datasets.
    • Click on the Correlated Genes Tab to view other genes with correlated expression patterns.
    • Utilize Tabs to see the gene in the Genome Browser, the Compare Region Viewer, associated Pathways, and Literature.
    • Using buttons on the left, add the gene to your Workspace, or view the NT and/or AA sequences.

How do I use the Gene List Heatmap Tab?

The Heatmap Tab visually displays expression levels of all the genes in a Gene List across all selected comparisons using a Heatmap Viewer where coloring is based on the Log Ratio value of a gene in a given comparison. It allows you to quickly find genes with similar expression patterns across one or more comparisons.

  • Use the Heatmap Toolbar located in the light blue row to:
    • Flip Axes: By default, Comparisons are displayed along the X axis and Genes are displayed along the Y axis. Additionally, the scale of rows and columns may be controlled by sliding the x and/or y slidebars located at the axis intersection in the upper left corner of the Heatmap.
    • Select Heatmap Color Scheme:
      • Red-Black-Green: Up regulated genes are red and down regulated genes are green. The brighter the color, the more differentially expressed a gene is. All the genes that do not pass the current Log Ratio cut-off are black.
      • Red-White-Blue: Up regulated genes are red and down regulated genes are blue. The brighter the color, the more differentially expressed a gene is. All the genes that do not pass the current Log Ratio cut-off are white.
    • Press the Cluster button to reorder genes and comparisons in the Heatmap, allowing for quick visual detection of genes with similar expression patterns across one or more comparisons. This default mode of clustering uses Person correlation for distance measure and the pairwise complete-linkage method for hierarchical clustering.
    • Press the Advance Clustering button to choose from various clustering algorithms and types.
    • Show Significant Genes/All Genes: Choose to display either only Significant Genes passing Log Ratio and Z-score cut-offs or All Genes in the Heatmap. With All Genes selected and ordered based on genomic positions or locus tags, you may quickly find genomic regions that are differentially/similarly expressed across one or more comparisons.
  • The following options may be accessed from a pop-up widow by clicking on any individual colored cell, any Gene label, or any Comparison label within the Heatmap. The same information can be collected for a whole region of interest within the Heatmap by clicking and dragging to select a group of cells.
    • Download expression data (Heatmap Data) for selected region.
    • Download the list of genes as an Excel or txt file.
    • Show Genes as an interactive Feature Table where the Table toolbar allows for sorting, downloading, and various analyses. For more details on how to use a Feature Table, see Feature Table FAQs.
    • Add Genes to a Group in your personal Workspace for future access.