Comparative Pathway Heatmap¶
Accessing the Comparative Pathway Heatmap on the PATRIC Website¶
This tool is accessible via the “Heatmap” Tab, which is accessed by clicking on any Pathway Name in the initial search results page generated within our Comparative pathway Tool. For information on how to use the Comparative pathway Tool please see Comparative Pathway Tool FAQs.
Comparative Pathway Heatmap Overview¶
The Heatmap is an interactive visualization tool, which provides an overview of the distribution of genomes across the set of EC numbers within a selected pathway. Patterns visible in a Heatmap can allow for many types of analysis such as, a bird’s-eye view of the conservation (or lack thereof) of particular genes of interest, discerning how many proteins have the same function within a single genome, and identifying proteins with multiple homologs or paralogs across a set of genomes.
Each cell is colored according to how many proteins (features) from a specific genome are assigned a particular EC number. Black cells indicate that there are no representative proteins from a specific genome assigned that EC number. Bright yellow cells indicate there is one representative protein, dark yellow cells indicate there are two representative proteins, and dark orange cells indicate there are three or more representative proteins.
- The entire visualization may be filtered by annotation source. To do this, chose an annotation source from the dropdown menu at the top of the Heatmap. Note: If you changed the annotation source from the default source, PATRIC, on the KEGG Map tab, then your new selection will also be the default when you click on the Heatmap tab.
- Each individual column or row within the Heatmap may be clicked and dragged to any specified position.
Comparative Pathway Heatmap Features and Functionality¶
- EC Numbers and Descriptions are listed along the Y (vertical) axis and corresponding Genomes are listed along the X (horizontal) axis. The scale of these 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.
- The following options may be accessed from a pop-up widow by
clicking on any individual colored cell, any EC label, or any Genome
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.
- The “Download Heatmap Data” button will show the count of representative features from each genome assigned to each EC Number in either a text or excel file. Note: Clicking this button from a EC label will produce a file with the count for each genome assigned to that EC number, while clicking on this button from a Genome label will produce a file with the count for that particular genome in every EC number associated with your selected pathway.
- The “Add Proteins to Group” button will save selected items to new, or existing, groups within your Workspace. To learn more about how to save data for future visits and utilize your personal Workspace please see Workspace FAQs.
- Data for each protein (feature), such as Genome Name, Accession
Number, Locus Tag, Start and End designations, and Overall
Length may be obtained in several ways:
- Clicking the “Download Proteins” button will open the protein data in either a text or excel file.
- Clicking the “Show Proteins” button will open the protein
data within a Pathways Table, where the Toolbar, located in
the light blue row of the table may be utilized 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 please see Workspace FAQs.
- View or download selected DNA and/or protein sequence data in FASTA format. The table itself, or selected data within it, are also downloadable in both excel and txt file formats.
- View pathways and associated pathway information for your selected genomes by clicking the Pathway Summary button.
- Conduct Multiple Sequence Alignment analysis on selected features 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 features by clicking the Map IDs button. For more information on this tool please see ID Mapping FAQs.
Note: All tables accessed via the Comparative Pathway Heatmap may be sorted as described in Feature Table FAQs.