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O04 Draw VENN Diagram between Three Closely Related Genomes

** What is Venn diagram?

- The Venn diagram is a figure that is used in the set theory and shows the distribution of numbers of elements in each set among three set (drawing of the diagram of four sets is also possible, however the IMC provide the Venn diagram of three sets or two. The diagram shows the set elements in circles and intersections are defined as the common elements. One of its applications is the Venn diagram of common genes and unique genes among closely related genomes in biology.

** Implemented Software Packages

  • - IMC GE and AE
  • - GT

** Functions

By using the already annotated sequence files in GenBank or EMBL format, the Venn diagram detects the common genes and unique genes between three genomes and draw the graphical image.

- Amino acid homology search is performed to get criteria information for detecting common genes.

- For the common gene criteria, "Percent Identity" and "Overlap Length" of the pairwise alignment between each gene in a pair.

- Let define that each pair of the genes are mutually common genes if the "Percent Identity" and the "Overlap Length" between the two genes satisfy the criteria.

*** Color Graphical drawing of the "Venn Diagram"

  • -- Clicking the counts of genes pops up the corresponding list of the genes.
  • -- Change of drawing color
  • -- Printing of the image

*** Listing of the common genes and file output

  • -- List and count of the common genes between three genomes.
  • -- List and count of the common genes between any two genomes.
  • -- List and count of unique genes that have no homologous gene in the counter genomes for each of the genomes.
  • -- Each gene list can be output as a CSV format file.

*** Common genes can be aligned in "Multiple Genome Viewer"

  • - Common genes can be graphically aligned in the MGV ("Multiple Genome Viewer" = previously called "Reference Genome Map") by clicking one of common genes in the common gene list.

** Restrictions

  • - The "Venn Diagram" function is implemented in the IMC AE and IMC GE.
  • - The genomes to be compared must be loaded in the "Multiple Genome Viewer".
  • -- This requirement is due to the co-moving function of the common gene list and the "Multiple Genome Viewer".

** Result dialog items explained

  • - [[View the result dialog>IMC_VennDiagramResultDialogEN]]
  • - [[View the gene list>IMC_VennDiagramResultListEN]]

** Operations

*** Preparation

  • - Before executing the Venn diagram, loading of two or more related genome sequence files in GenBank format in the "Multiple Genome Viewer (Reference Map)" is necessary.
  • -- The "Multiple Genome Viewer" is used to present the aligned views of the common genes.
  • IMC_5.0.6_BX22001.JPG

*** How to operate the Venn diagram

  • 1. Click "Venn Diagram" button in the tool box.
    • -- The "Venn Diagram Setting" dialog is displayed.
    • -- The loaded file list of "Multiple Genome Viewer(MGV) Map" is shown in the dialog.
    • IMC_5.0.12_BZ29_012.JPG
  • 2. Check up to three genome files from the list.
    • imcimgO/IMC_5.0.12_BZ29_008.JPG
  • 3. Click "Set".
    • -- The "Venn Diagram" is launched and a progress message is displayed during the execution.
    • IMC_5.0.6_BX22004.JPG
    • -- It takes a few minutes or larger genomes more than 10 minutes to complete the process.
    • -- Upon finished, the "Venn Diagram" result dialog is displayed.
  • IMC_5.0.6_BX22006.JPG

*** Operations on the Result Dialog

  • 1.  Click one of the tab on the top of the dialog.
    • This switches the tab panels.
    • IMC_5.0.6_BX22018.JPG
  • 2. Click "genome1-genome2-genome3" tab.
    • -- This opens the common gene and unique gene lists among the three genomes
    • IMC_5.0.6_BX22012.JPG
    • IMC_VennDiagramResultDialog
  • 3. Click "genome1-genome2" tab.
    • -- This opens the common gene and unique gene lists between any one pairwise sets of the three genomes.
    • IMC_VennDiagramResultList
    • IMC_5.0.6_BX22014.JPG

*** Change in the drawing color of "Venn Diagram"

  • - The below colors can be changed.
  • -- Color of the genome 1
  • -- Color of the genome 2
  • -- Color of the genome 3
  • -- Color of the numeric characters
  • IMC_5.0.6_BX22020.JPG
  • 1. Click a color box.
    • -- The color palette is displayed.
    • IMC_5.0.6_BX22024.JPG
  • 2. Pick a different color from the color palette.
  • -- The color is changed.
    • IMC_5.0.6_BX22025.JPG
  • 3. Click "Show".
    • -- The selected color is reflected and the Venn diagram is redrawn.
    • IMC_5.0.6_BX22026.JPG

*** Common Gene Links to MGV and their local alignment

  • 1. Clicking the one of the entries of the common genes, the corresponding position of the target genome is located and shown in the map of the Multiple Genome Viewer.
  • IMC_5.0.6_BX22031.JPG
  • 2. - Clicking one of the common genes unique genes between arbitrary two genomes of the three makes the gene to be highlighted in the "Multiple Genome Viewer"
  • IMC_5.0.6_BX22032.JPG
*** Printing of the image of the Venn diagram

  • 1. Clicking one of the buttons placed in the bottom of the "Venn Diagram" result dialog.
    • IMC_5.0.2_B910004.JPG
    • i) Change the page settings --> Click [["Page Setup">IMC_ButtonSetup]].
    • ii) Direct printing to the default printer --> Click [["Print">IMC_ButtonPrint]].
    • iii) Image file output in [[PDF]] format --> Click [["PDF">IMC_ButtonPDF]].
    • iv) Image file output in [[PNG]] format --> Click [["PNG">IMC_ButtonPNG]].
    • v) Image file output in [[EMF]] format --> Click [["EMF">IMC_ButtonEMF]].

*** List Output

  • 1.  Click "CSV" after selecting one of the tab panel of the common genes.
    • IMC_5.0.2_B910005.JPG
    • -- A file selection dialog is displayed.
  • 2. Specify the output file name and its directory name.
    • -- The output file can be browsed or edited by MS Excel.

*** Load and display a past result of the VENN diagram.

  • 1. Click "VENN Diagram" execution button.
    • -- The "VENN Diagram" dialog is displayed.
  • IMC_5.0.12_BZ29_012.JPG);
  • 2. Click "Read...".
    • -- The File Chooser is displayed.
  • IMC_5.0.12_BZ29_004.JPG
  • 3. Select one of the result files of the VENN diagram.
    • -- The confirm message is displayed.
    • IMC_5.0.12_BZ29_006.JPG
  • 4. Click "Yes(Y)".
    • -- The selected file is loaded and displayed.
    • IMC_5.0.12_BZ29_014.JPG

** Algorithm

  • - All the amino acid sequence of the CDS of one genome are compared with one of the other genomes using Blast homology search.
  • - If one of the CDS's top hit to the CDS on the another genome, also be a top hit to the exact CDS of the original genome, these two genes are defined common genes or ortholog genes under the condition below.
  • -- These pair must exceed the threshold value of "Percent Identity" and "Overlap Length".

** Bug Reports

*** Unfixed Bugs

  • - No bug is reported.

*** Fixed Bugs

  • IMC Version 5.0.4, released on 2011/9/20
    • -- The bug that occurred when the selected qualifier for the common gene identification contains a space character, is fixed.
  • IMC Version 5.0.2, released on 2011/9/10
    • -- The bug of appearing of minus value as the count of common genes in the graphical view of the "VENN Diagram".

** Recent Enhancements and Modifications

*** The improvements in the IMC version 5.0.11 that was released on 2011/12/20,

  • 1. The selection method of the target files of the VENN Diagram, is changed.

    • -- Previously, the target files are selected directly using a file chooser.
    • -- From now on, the target files are selected from the MGV loaded file list in the VENN diagram.

*** The improvements in the IMC version 5.0.10 that was released on 2011/12/6, are as follows.

  • 1. A result of a VENN Diagram can be saved in a file so that it can be referred later.
    • -- In case that the genome files are not loaded in the MGV, these files are automatically loaded in the MGV. However, if the names or locations of the files were changed, these files cannot be referred.

*** The major enhancement items in the IMC version 4.3.11 that was released on 2011/6/1,

  • + Unless two of more genomes are loaded in the MGV(old name = reference map), Venn Diagram can not be executed.
  • + The file names of the target genomes are displayed.
  • + The font used in the diagram becomes larger.
  • + For the drawing circles of the diagram, the frame line becomes thicker and paint color becomes paler.
  • + Clicking the gene counter digits, opens the corresponding tab panel.
  • + Clicking one of the common gene pair or threesome brings the genome map on the the multiple genome viewer to the exact position of the common gene and locally aligned.
  • ~
  • + The common gene determinant criteria is changed from using e-value to Percent Identity and Overlap Ratio.
  • -- The parameters, "Percent Identity" and "Overlap Ratio" can be changed from the menu, "Option Setting" → "Option" → "Venn Diagram".
  • + A sequential number column is added in the common gene list.
  • + Common gene position in the genome is added in the list.
  • + List of unique genes that has no common genes in the other two genome is generated.
  • + Lists of common genes between two of the three genomes are generated.

** Future Enhancements

  • - Links to the external databases.
  • - The reservation and the restoration functions of the whole results.

** Related Functions

  • IMC_DotPlot
  • IMC_GenomeRearrangementMap
  • IMC_LocalGenomeRearrangementMap

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